dr hab. Rafał Milanowski, prof. ucz. (dyrektor Instytutu Biologii Ewolucyjnej)

@article{Mikina2024,

title = {Transposon-derived introns as an element shaping the structure of eukaryotic genomes},

author = {Weronika Mikina and Paweł Hałakuc and Rafał Milanowski},

doi = {10.1186/s13100-024-00325-w},

issn = {1759-8753},

year  = {2024},

date = {2024-07-27},

urldate = {2024-12-00},

journal = {Mobile DNA},

volume = {15},

pages = {15},

publisher = {Springer Science and Business Media LLC},

abstract = {The widely accepted hypothesis postulates that the first spliceosomal introns originated from group II self-splicing introns. However, it is evident that not all spliceosomal introns in the nuclear genes of modern eukaryotes are inherited through vertical transfer of intronic sequences. Several phenomena contribute to the formation of new introns but their most common origin seems to be the insertion of transposable elements. Recent analyses have highlighted instances of mass gains of new introns from transposable elements. These events often coincide with an increase or change in the spliceosome's tolerance to splicing signals, including the acceptance of noncanonical borders. Widespread acquisitions of transposon-derived introns occur across diverse evolutionary lineages, indicating convergent processes. These events, though independent, likely require a similar set of conditions. These conditions include the presence of transposon elements with features enabling their removal at the RNA level as introns and/or the existence of a splicing mechanism capable of excising unusual sequences that would otherwise not be recognized as introns by standard splicing machinery. Herein we summarize those mechanisms across different eukaryotic lineages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GUMINSKA2024126033,

title = {Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions},

author = {Natalia Gumińska and Paweł Hałakuc and Bożena Zakryś and Rafał Milanowski},

url = {https://www.sciencedirect.com/science/article/pii/S1434461024000257},

doi = {https://doi.org/10.1016/j.protis.2024.126033},

issn = {1434-4610},

year  = {2024},

date = {2024-04-03},

urldate = {2024-01-01},

journal = {Protist},

volume = {175},

number = {3},

pages = {126033},

abstract = {Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224–5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{JANKOWSKA2024126024,

title = {Biodiversity of autotrophic euglenids based on the group specific DNA metabarcoding approach},

author = {Katarzyna Jankowska and Maja Łukomska-Kowalczyk and Rafał Milanowski and Alicja Fells and Bożena Zakryś},

url = {https://www.sciencedirect.com/science/article/pii/S1434461024000166},

doi = {https://doi.org/10.1016/j.protis.2024.126024},

issn = {1434-4610},

year  = {2024},

date = {2024-03-04},

urldate = {2024-01-01},

journal = {Protist},

volume = {175},

number = {3},

pages = {126024},

abstract = {This study reports a comprehensive analysis of photoautotrophic euglenids’ distribution and biodiversity in 16 small water bodies of various types (including fish ponds, field ponds, rural ponds and park ponds) located in three regions of Poland: Masovia, Masuria and Pomerania during a period of three years. By employing a euglenid specific barcode marker and a curated database of V2 18S rDNA sequences it was possible to identify 97.7 % of euglenid reads at species level. A total of 152 species classified in 13 genera were identified. The number of euglenid species found in one pond varied from 40 to 102. The most common species were Euglena agilis and Euglenaria caudata, found in every analysed waterbody. The highest number of observed species belonged to Trachelomonas and Phacus. Certain species exhibited a tendency to coexist, suggesting the presence of distinct species assemblages. Among them, the most distinctive cluster was associated with water bodies located in the Masuria region, characterized also by the greatest species richness, including many very rare species: Euglenaformis chlorophoenicea, Lepocinclis autumnalis, L. marssonii, Trachelomonas eurystoma, T. manschurica, T. mucosa, T. zuberi, T. zuberi var. nepos.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/tax.12937,

title = {Molecular and morphological delimitation of species in Strombomonas (Euglenaceae) including a protocol for DNA isolation utilising a chelating resin},

author = {Alicja Fells and Xiaodie Jiang and Katarzyna Jankowska and Maja Łukomska-Kowalczyk and Rafał Milanowski and Quanxi Wang and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tax.12937},

doi = {https://doi.org/10.1002/tax.12937},

year  = {2023},

date = {2023-08-11},

urldate = {2023-01-01},

journal = {TAXON},

volume = {72},

number = {4},

pages = {733-750},

abstract = {Abstract Although Strombomonas verrucosa has been the type of the genus name for almost 100 years, its lack of clear diagnostic traits has rendered morphological distinction from its congeners almost impossible. As such, a study was conducted combining previously unused morphological data (chloroplast characters) with molecular data (sequences of nuclear SSU, LSU and plastid-encoded SSU rDNA) and extensive literature review. The study focused on environmental samples obtained from Poland and China and resulted in 51 new sequences representing three molecular markers (17 nSSU, 16 nLSU and 18 cpSSU rDNA). Revised delimitations of the genus Strombomonas and its type S. verrucosa are presented that include new and detailed diagnostic characters. In addition to the type, we recognize nine species: S. acuminata, S. borystheniensis, S. eurystoma, S. fluviatilis, S. gibberosa, S. maxima, S. ovalis, S. schauinslandii, S. triquetra. Three of these are incorporated into a phylogeny for the first time (S. fluviatilis, S. gibberosa, S. schauinslandii). To improve the efficiency of DNA isolation from loricate cells, a protocol utilising a chelating resin for DNA isolation – following the lead of diatomologists – has been adjusted for Euglenaceae and is also presented.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jagielska23_1,

title = {Mitochondrial genomes – unity and diversity},

author = {Maria Jagielska and Paweł Hałakuc and Magdalena Płecha and Rafał Milanowski},

url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/486},

doi = {10.18388/pb.2021_486 },

year  = {2023},

date = {2023-06-19},

journal = {Postępy Biochemii},

volume = {69},

number = {2},

pages = {113-121},

abstract = {The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene trans-fers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gumin2022Char,

title = {Charakterystyka kolistych DNA u Eukarya},

author = {Natalia Gumińska and Rafał Milanowski},

url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/423},

doi = {10.18388/pb.2021_423 },

issn = {2720-5959},

year  = {2022},

date = {2022-07-06},

journal = {Postępy Biochemii},

volume = {68},

number = {2},

pages = {129-141},

abstract = {W komórkach eukariotycznych DNA występuje głównie w formie liniowej, upakowanej w chromosomy. Poza tym może też przybierać postać kolistych cząsteczek. Najdokładniej zbadane zostały koliste DNA odgrywające rolę genomów mitochondriów i chloroplastów. Niemniej zasób kolistych DNA u Eukarya jest znacznie szerszy. Obejmuje również pozachromosomowe cząsteczki (ang. extrachromosomal circular DNA; eccDNA): koliste formy rDNA, pierścienie telomerowe, małe polidyspersyjne DNA, mikroDNA oraz inne typy kolistych DNA o pochodzeniu jądrowym. Występowanie eccDNA potwierdzono u wszystkich organizmów testowanych w tym zakresie. Dotychczasowe badania wykazały, że niektóre eccDNA są obecne na każdym etapie cyklu komórkowego, podczas gdy inne pojawiają się i/lub ulegają nagromadzeniu w szczególnych okolicznościach. Dowiedziono, że akumulacja eccDNA nierzadko zachodzi w następstwie poważnej destabilizacji genomu, będącej wynikiem stanów chorobowych czy stresu. Choć w środowisku naukowym wzrasta zainteresowanie eccDNA, pozostają one słabo poznanym składnikiem genomów eukariotycznych. Nadal niewiele wiadomo na temat mechanizmów ich formowania, ewolucji oraz ich funkcji biologicznych.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Haakuc2022,

title = {Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans},

author = {Paweł Hałakuc and Anna Karnkowska and Rafał Milanowski},

url = {https://doi.org/10.1186/s12862-022-02014-9

https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-022-02014-9},

doi = {10.1186/s12862-022-02014-9},

issn = {2730-7182},

year  = {2022},

date = {2022-05-09},

journal = {BMC Ecology and Evolution},

volume = {22},

number = {1},

pages = {59},

abstract = {Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/jpy.13220,

title = {Toward the robust resolution of taxonomic ambiguity within Lepocinclis (Euglenida) based on DNA sequencing and morphology},

author = {Katarzyna Chaber and Maja Łukomska-Kowalczyk and Alicja Fells and Rafał Milanowski and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13220},

doi = {https://doi.org/10.1111/jpy.13220},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Phycology},

volume = {58},

number = {1},

pages = {105-120},

abstract = {DNA sequences were analyzed for three groups of species from the Lepocinclis genus (L. acus-like, L. oxyuris-like, and L. tripteris-like) along with cellular morphology. Phylogenetic analyses were based on nuclear SSU rDNA, LSU rDNA, and plastid-encoded LSU rDNA. DNA sequences were obtained from species available in culture collections (L. acus SAG 1224-1a and UTEX 1316) and those isolated directly from the environment in Poland (48 isolates), resulting in 79 new sequences. The obtained phylogenetic tree of Lepocinclis included 27 taxa, five of which are presented for the first time (L. convoluta, L. gracillimoides, L. longissima, L. pseudospiroides, and L. torta) and nine taxonomically verified and described. Based on morphology, literature data, and phylogenetic analyses, the following species were distinguished: in the L. acus-like group, L. longissima and L. acus; in the L. tripteris-like group, L. pseudospiroides, L. torta, and L. tripteris; in the L. oxyuris-like group, L. gracillimoides, L. oxyuris var. oxyuris, and L. oxyuris var. helicoidea. For all verified species, diagnostic descriptions were emended, nomenclatural adjustments were made, and epitypes were designated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Soukal2021,

title = {Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology},

author = {Petr Soukal and Štěpánka Hrdá and Anna Karnkowska and Rafał Milanowski and Jana Szabová and Miluše Hradilová and Hynek Strnad and Čestmír Vlček and Ivan Čepička and Vladimír Hampl},

url = {https://doi.org/10.1038/s41598-021-92174-3 

http://www.nature.com/articles/s41598-021-92174-3},

doi = {10.1038/s41598-021-92174-3},

issn = {2045-2322},

year  = {2021},

date = {2021-12-01},

journal = {Scientific Reports},

volume = {11},

number = {1},

pages = {13070},

abstract = {Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata . The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis . Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata , which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis . The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/1462-2920.15495,

title = {Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids},

author = {Natalia Gumińska and Maja Łukomska-Kowalczyk and Katarzyna Chaber and Bożena Zakryś and Rafał Milanowski},

url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15495},

doi = {https://doi.org/10.1111/1462-2920.15495},

year  = {2021},

date = {2021-04-08},

journal = {Environmental Microbiology},

volume = {23},

number = {6},

pages = {2992–3008 },

abstract = {Summary Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species-level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB-based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GUMINSKA2021166758,

title = {A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids},

author = {Natalia Gumińska and Bożena Zakryś and Rafał Milanowski},

url = {https://www.sciencedirect.com/science/article/pii/S0022283620306835?via%3Dihub},

doi = {https://doi.org/10.1016/j.jmb.2020.166758},

year  = {2021},

date = {2021-02-05},

journal = {Journal of Molecular Biology},

volume = {433},

number = {3},

pages = {166758},

abstract = {Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringing together intron ends and placing adjacent exons in proximity. To date, little is known about the mechanism of their excision (e.g. whether it involves the spliceosome or not). The tubA gene of Euglena gracilis harbors three conventional and three nonconventional introns. While the conventional introns are excised as lariats, nonconventional introns are present in the cell solely as circular RNAs with full-length ends. Based on this discovery as well as on previous observations indicating that nonconventional introns are observed frequently at unique positions of genes, we suggest that this new type of intronic circRNA might play a role in intron mobility.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/jpy.13107,

title = {Description of Flexiglena gen. nov. and new members of Discoplastis and Euglenaformis (Euglenida)},

author = {Maja Łukomska-Kowalczyk and Katarzyna Chaber and Alicja Fells and Rafał Milanowski and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13107},

doi = {https://doi.org/10.1111/jpy.13107},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Phycology},

volume = {57},

number = {3},

pages = {766-779},

abstract = {Environmental sampling in Poland and the United States and phylogenetic analyses based on 567 sequences of four genes (155 sequences of nuclear SSU rDNA, 139 of nuclear LSU rDNA, 135 of plastid-encoded SSU rDNA, and 138 of plastid-encoded LSU rDNA) resulted in description of the new genus Flexiglena, which has been erected by accommodating Euglena variabilis, and enriching the Discoplastis and Euglenaformis genera with five new species. Four of them have joined the Discoplastis genus, currently consisting of six representatives: D. adunca, D. angusta (=Euglena angusta), D. constricta (=Lepocinclis constricta), D. excavata (=E. excavata), D. gasterosteus (=E. gasterosteus), and D. spathirhyncha. One of them has enriched the Euglenaformis genus, currently represented by two species: Euf. chlorophoenicea (= E. chlorophoenicea) and Euf. proxima. For most studied species, the diagnostic descriptions have been emended and epitypes were designated. Furthermore, the emending of Discoplastis and Euglenaformis diagnoses was performed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/jpy.13028,

title = {Taxon‐rich phylogeny and taxonomy of the genus Phacus (Euglenida) based on morphological and molecular data },

author = {Maja Łukomska-Kowalczyk and Alicja Fells and Katarzyna Chaber and Rafał Milanowski and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/10.1111/jpy.13028},

doi = { https://doi.org/10.1111/jpy.13028},

year  = {2020},

date = {2020-05-19},

journal = {Journal of Phycology},

volume = {56},

number = {5},

pages = {1135-1156},

abstract = {Morphological and molecular features were analyzed for a species of Phacus to better understand the phylogenetic relationships among them and establish the taxonomy. Phylogenetic analyses were based on nSSU rDNA and the research resulted in 55 new sequences. The study included species available in algal collections and those isolated directly from the environment in Poland and the Czech Republic. As a result, the obtained phylogenetic tree of Phacus includes 50 species, out of which 7 are represented on a tree for the first time (Phacus anacoelus, P. anomalus, P. curvicauda, P. elegans, P. lismorensis, P. minutus and P. stokesii) and many have been taxonomically verified. For all verified species, diagnostic descriptions were amended, the naming was reordered and epitypes were designated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/jpy.12949,

title = {Molecular and Morphological Delimitation of Species in the Group of Lepocinclis Ovum-like taxa (Euglenida)},

author = {Maja Łukomska-Kowalczyk and Katarzyna Chaber and Alicja Fells and Rafał Milanowski and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12949},

doi = {https://doi.org/10.1111/jpy.12949},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Phycology},

volume = {56},

number = {2},

pages = {283-299},

abstract = {Although Lepocinclis ovum is recognized as a cosmopolitan and common species, and Lepocinclis globulus is the type species of the genus Lepocinclis, their correct identification is nearly impossible. The reason is that over 30 morphologically similar taxa appear in the literature, but no good diagnostic features exist to distinguish amongst them. Using environmental sampling and nuclear SSU rDNA sequencing, we delimited species within the group of Lepocinclis ovum-like taxa. Morphological and molecular features were analyzed for taxa isolated from Poland and six cultured strains from algal collections. In the case of environmental sampling, DNA was obtained from a small number of cells (20–400) isolated with a micropipette without setting up laboratory cultures (52 isolates), and phylogenetic analyses were based on the variation in nSSU rDNA. Apart from L. ovum and L. globulus, 13 other species were distinguished and four taxa (Lepocinclis conica comb. nov., L. fominii comb. nov., L. gracilicauda comb. nov., and L. pseudofominii nom. nov.) had their taxonomic ranks changed. For all verified species, diagnostic descriptions were emended and epitypes designated. The only exception was L. ovum, for which the epitype was questioned and thus, a new candidate for the epitype was suggested for future adoption.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ignatenko2019,

title = {Mechanizmy utraty i nabywania intronów spliceosomalnych},

author = {Antonina Ignatenko and Natalia Gumińska and Rafał Milanowski},

url = {https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/292},

doi = {10.18388/pb.2019_292},

issn = {00325422},

year  = {2019},

date = {2019-01-01},

journal = {Postepy biochemii},

volume = {65},

number = {4},

pages = {289--298},

abstract = {Introny to wewnątrzgenowe sekwencje niekodujące. Dawniej były uznawane za „śmieciowy” DNA, jednak obecnie uważa się, że są ważnymi elementami wpływającymi na funkcjonowanie genomu. Udowodniono, że introny zwiększają różnorodność transkryptomu i proteomu, spełniają w komórce role regulatorowe, wpływają na ekspresję genów oraz obróbkę, translację i degradację mRNA. Ze względu na sposób powstawania dzielą się na trzy główne kategorie: spliceosomalne, samowycinające się oraz introny tRNA. Introny spliceosomalne są charakterystyczne dla organizmów eukariotycznych. Analizy sekwencji genów ortologicznych w rożnych grupach eukariontów pozwoliły zidentyfikować wiele przypadków nabywania oraz utraty intronów. Niektóre z tych zdarzeń miały miejsce w dalekiej przeszłości, do innych doszło stosunkowo niedawno. Uważa się, że procesy te mogą działać jako jedna z sił napędowych w ewolucji genów eukariotycznych.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kulczycka2018,

title = {PCR identification of toxic euglenid species Euglena sanguinea},

author = {Agata Kulczycka and Maja Łukomska-Kowalczyk and Bożena Zakryś and Rafał Milanowski},

url = {http://link.springer.com/10.1007/s10811-017-1376-z},

doi = {10.1007/s10811-017-1376-z},

issn = {0921-8971},

year  = {2018},

date = {2018-06-01},

journal = {Journal of Applied Phycology},

volume = {30},

number = {3},

pages = {1759--1763},

abstract = {textcopyright 2018 The Author(s) Euglena sanguinea Ehrenberg is the only known species of euglenids which forms toxic blooms causing tangible losses to fish farms. Euglena sanguinea produces euglenophycin, a toxin similar in structure to solenopsin, an alkaloid found in fire ant venom. It was proved that euglenophycin exhibits not only ichthyotoxic but also herbicidal and anticancer activity. Recently, a specific mass spectrometric method of identification and quantitation of euglenophycin was developed to facilitate monitoring of that toxin in freshwater ponds. Despite the recent taxonomic verifications, proper identification of E. sanguinea is still difficult, especially for less experienced researchers. Herein, we describe a simple method based on nested PCR amplification of the nSSU rDNA fragments to identify a single E. sanguinea cell and its detection in a sample of water. The method will further facilitate monitoring of water reservoirs, especially estimating the risk of toxic blooms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guminska2018,

title = {Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids},

author = {Natalia Gumińska and Magdalena Płecha and Halszka Walkiewicz and Paweł Hałakuc and Bożena Zakryś and Rafał Milanowski},

url = {https://doi.org/10.1007/s10811-018-1496-0},

doi = {10.1007/s10811-018-1496-0},

issn = {1573-5176},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Applied Phycology},

volume = {30},

number = {6},

pages = {3541--3549},

abstract = {In the present study, five different DNA extraction procedures were examined to determine their effectiveness for extracting DNA suitable for NGS applications. This included two silica-membrane spin column kits, phenol:chloroform, and two CTAB-based methods. Spectrophotometric and fluorimetric measurements as well as standard gel electrophoresis were used as criteria for evaluating the quantity and quality of the isolated DNA prior to the sequencing. Herein, the method of establishing and maintaining axenic Euglena cultures is also presented. The modified CTAB-based method proved to be highly efficient. In terms of DNA quantity and purity (according to the absorbance ratios), the chosen method resulted in DNA of high molecular weight and quality, which fulfills the library construction requirements. Genomic DNA of Euglena hiemalis (CCAP 1224/35) and E. longa (CCAP 1204-17a) isolated using the suggested protocol had been successfully sequenced on the Illumina HiSeq platform. A modified, rapid CTAB-based method of total DNA isolation from Euglena has been described. In terms of the DNA quantity and quality, the protocol devised involving the washing step with DMSO:acetonitrile proved superior to the commonly used, commercially manufactured kits and isolation with phenol:chloroform. The method is also less labor-intensive and time-consuming than the traditional CTAB-based protocol.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guminska2018b,

title = {Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis},

author = {Natalia Gumińska and Magdalena Płecha and Bożena Zakryś and Rafał Milanowski},

doi = {10.1371/journal.pgen.1007761},

issn = {15537404},

year  = {2018},

date = {2018-01-01},

journal = {PLoS Genetics},

volume = {14},

number = {10},

pages = {e1007761},

abstract = {Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zganiacz2017,

title = {Charakterystyka kolistych cząsteczek kwasów rybonukleinowych (circRNA) },

author = {Daria Zganiacz and Rafał Milanowski},

url = {http://www.ncbi.nlm.nih.gov/pubmed/29294267

https://postepybiochemii.ptbioch.edu.pl/index.php/PB/article/view/77},

issn = {0032-5422},

year  = {2017},

date = {2017-01-01},

journal = {Postepy biochemii},

volume = {63},

number = {3},

pages = {221--232},

abstract = {Kwasy rybonukleinowe wystcepujca w różnych formach, micedzy innymi w kolistej (circRNA). Forma kolista RNA jest znacznie bardziej rozpowszechniona niż pierwotnie scadzono. U wirusa HDV, wiroidów oraz wiroidopodobnych satelitarnych RNA pełni funkcjce genomu. Koliste RNA zaobserwowano w zwicazku z dojrzewaniem prekursorów rRNA i tRNA niektórych archeonów. Może wystcepować jako produkt końcowy (introny) lub stadium przejściowe. U archeonów odnotowano również formy koliste kilku snoRNA oraz innych RNA pełnicacych funkcje regulacyjne. Zauważono powstawanie circRNA w zwicazku z dojrzewaniem pre-mRNA zawierajcacych introny spliceosomalne, grupy I oraz grupy II. Zaobserwowane czcasteczki składały sice z sekwencji samych intronów, samych eksonów lub obu rodzajów na raz. Intronowe circRNA mogca być powicazane z mobilnościca tychże elementów genetycznych. Eksonowe (wystcepujca u eukariontów) czcesto sca tkankowo specyficzne lub charakterystyczne dla określonego etapu rozwoju organizmu; niektóre sca zdolne do modulacji działania miRNA. Przypuszcza sice też, że sca powicazane z kilkoma chorobami neurodegeneracyjnymi. Koliste RNA sca potencjalnie użyteczne terapeutycznie i w diagnostyce.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ukomska-Kowalczyk2016,

title = {DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA},

author = {Maja Łukomska-Kowalczyk and Anna Karnkowska and Małgorzata Krupska and Rafał Milanowski and Bożena Zakryś},

editor = {T Mock},

url = {http://doi.wiley.com/10.1111/jpy.12439},

doi = {10.1111/jpy.12439},

issn = {00223646},

year  = {2016},

date = {2016-12-01},

journal = {Journal of Phycology},

volume = {52},

number = {6},

pages = {951--960},

abstract = {textcopyright 2016 Phycological Society of America. Autotrophic euglenids (Euglenophyceae) are a common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step toward the molecular identification of autotrophic euglenids. Based on the literature, we selected verified species and used a plethora of available me thods to validate two molecular markers: COI and 18S rDNA (the whole sequence and three fragments separately) as potential DNA barcodes. Analyses of the COI gene were performed based on the data set of 43 sequences (42 obtained in this study) representing 24 species and the COI gene was discarded as a DNA barcode mainly due to a lack of universal primer sites. For 18S rDNA analyses we used a data set containing 263 sequences belonging to 86 taxonomically verified species. We demonstrated that the whole 18S rDNA is too long to be a useful marker, but from the three shorter analyzed variable regions we recommend variable regions V2V3 and V4 of 18S rDNA as autotrophic euglenid barcodes due to their high efficiency (above 95% and 90%, respectively).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Milanowski2016,

title = {Intermediate introns in nuclear genes of euglenids – are they a distinct type?},

author = {Rafał Milanowski and Natalia Gumińska and Anna Karnkowska and Takao Ishikawa and Bożena Zakryś},

url = {https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-016-0620-5},

doi = {10.1186/s12862-016-0620-5},

issn = {1471-2148},

year  = {2016},

date = {2016-12-01},

journal = {BMC Evolutionary Biology},

volume = {16},

number = {1},

pages = {49},

abstract = {textcopyright 2016 Milanowski et al. Background: Nuclear genes of euglenids contain two major types of introns: Conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one (intermediate/nonconventional subtype) or both (conventional/intermediate subtype) canonical spliceosomal borders. However, it has been also postulated that most introns classified as intermediate could simply be special cases of conventional or nonconventional introns. Results: Sequences of tubB, hsp90 and gapC genes from six strains of Euglena agilis were obtained. They contain four, six, and two or three introns, respectively (the third intron in the gapC gene is unique for just one strain). Conventional introns were present at three positions: Two in the tubB gene (at one position conventional/intermediate introns were also found) and one in the gapC gene. Nonconventional introns are present at ten positions: T wo in the tubB gene (at one position intermediate/nonconventional introns were also found), six in hsp90 (at four positions intermediate/nonconventional introns were also found), and two in the gapC gene. Conclusions: Sequence and RNA secondary structure analyses of nonconventional introns confirmed that their most strongly conserved elements are base pairing nucleotides at positions +4, +5 and +6/-8,-7 and-6 (in most introns CAG/CTG nucleotides were observed). It was also confirmed that the presence of the 5' GT/C end in intermediate/nonconventional introns is not the result of kinship with conventional introns, but is due to evolutionary pressure to preserve the purine at the 5' end. However, an example of a nonconventional intron with GC-AG ends was shown, suggesting the possibility of intron type conversion between nonconventional and conventional. Furthermore, an analysis of conventional introns revealed that the ability to form a stable RNA secondary structure by some introns is probably not a result of their relationship with nonconventional introns. It was also shown that acquisition of new nonconventional introns is an ongoing process and can be observed at the level of a single species. In the recently acquired intron in the gapC gene an extended direct repeats at the intron-exon junctions are present, suggesting that double-strand break repair process could be the source of new nonconventional introns.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ukomska-Kowalczyk2015,

title = {Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses},

author = {Maja Łukomska-Kowalczyk and Anna Karnkowska and Rafał Milanowski and Łukasz Łach and Bożena Zakryś},

editor = {O {De Clerck}},

url = {http://doi.wiley.com/10.1111/jpy.12352},

doi = {10.1111/jpy.12352},

issn = {00223646},

year  = {2015},

date = {2015-12-01},

journal = {Journal of Phycology},

volume = {51},

number = {6},

pages = {1147--1157},

abstract = {textcopyright 2015 Phycological Society of America. Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genome amplification, we delimited species within the Phacus longicauda complex. Morphological and molecular characters were analyzed for 36 strains isolated from environmental samples (mainly from Poland). DNA was obtained from a small number of cells (20-30) isolated with a micropipette from every sample (i.e., without setting up laboratory cultures), and phylogenetic analyses were based on variation in nSSU rDNA. Apart from Phacus longicauda, three other species (Phacus circumflexus, Phacus helikoides, and Phacus tortus) were distinguished. Phacus cordata comb. nov. Zakryś et M. łukomska and Phacus rotunda comb. nov. Zakryś et M. łukomska had their taxonomic ranks changed and two species new to science, Phacus cristatus sp. nov. Zakryś et M. łukomska and Phacus crassus sp. nov. Zakryś et M. łukomska, were described. For all verified species, diagnostic descriptions were amended and epitypes designated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Milanowski2014,

title = {Distribution of Conventional and Nonconventional Introns in Tubulin (alpha and beta) Genes of Euglenids},

author = {Rafał Milanowski and Anna Karnkowska and Takao Ishikawa and Bożena Zakryś},

url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mst227},

doi = {10.1093/molbev/mst227},

issn = {1537-1719},

year  = {2014},

date = {2014-03-01},

journal = {Molecular Biology and Evolution},

volume = {31},

number = {3},

pages = {584--593},

abstract = {The nuclear genomes of euglenids contain three types of introns: conventional spliceosomal introns, nonconventional introns for which a splicing mechanism is unknown (variable noncanonical borders, RNA secondary structure bringing together intron ends), and so-called intermediate introns, which combine features of conventional and nonconventional introns. Analysis of two genes, tubA and tubB, from 20 species of euglenids reveals contrasting distribution patterns of conventional and nonconventional introns - positions of conventional introns are conserved, whereas those of the nonconventional ones are unique to individual species or small groups of closely related taxa. Moreover, in the group of phototrophic euglenids, 11 events of conventional intron loss versus 15 events of nonconventional intron gain were identified. A comparison of all nonconventional intron sequences highlighted the most conserved elements in their sequence and secondary structure. Our results led us to put forward two hypotheses. 1) The first one posits that mutational changes in intron sequence could lead to a change in their excision mechanism - intermediate introns would then be a transitional form between the conventional and nonconventional introns. 2) The second hypothesis concerns the origin of nonconventional introns - because of the presence of inverted repeats near their ends, insertion of MITE-like transposon elements is proposed as a possible source of new introns. textcopyright 2013 The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zakrys2013,

title = {A new photosynthetic euglenoid isolated in Poland: Euglenaria clepsydroides sp. nov. (Euglenea)},

author = {Bożena Zakryś and Anna Karnkowska-Ishikawa and Maja Łukomska-Kowalczyk and Rafał Milanowski},

url = {https://www.tandfonline.com/doi/full/10.1080/09670262.2013.809479},

doi = {10.1080/09670262.2013.809479},

issn = {0967-0262},

year  = {2013},

date = {2013-08-01},

journal = {European Journal of Phycology},

volume = {48},

number = {3},

pages = {260--267},

abstract = {In this paper, we describe a new photosynthetic euglenoid species, Euglenaria clepsydroides Zakryś, sp. nov., found in Poland. A large population of this species exists in a few, small, eutrophic bodies of water inside the Masurian Landscape Park (covering a part of the Masurian Lake District in Poland). The characteristic and atypical (hourglass-like) cell shape sets it well apart from the other species that have been described up to now. This atypical cell shape has so far been observed only in three species - Lepocinclis constricta, Euglena undulata and Euglena gymnodinioides - whose other morphological characteristics, such as the number and morphology of chloroplasts, the lack of mucocysts, and nuclear SSU rDNA sequence data, exclude the possibility that they could be close relatives of Euglenaria clepsydroides. On the phylogenetic tree, the new species is situated within the Euglenaria clade. While it is a sister group of the clade that includes representatives of Euglenaria anabaena, the two species are clearly morphologically distinct. textcopyright 2013 Copyright British Phycological Society.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karnkowska-Ishikawa2013,

title = {A redescription of morphologically similar species from the genus Euglena : E. laciniata, E. sanguinea, E. sociabilis, and E. splendens 1},

author = {Anna Karnkowska-Ishikawa and Rafał Milanowski and Richard E Triemer and Bo}ena Zakryś},

editor = {K Valentin},

url = {http://doi.wiley.com/10.1111/jpy.12072},

doi = {10.1111/jpy.12072},

issn = {00223646},

year  = {2013},

date = {2013-06-01},

journal = {Journal of Phycology},

volume = {49},

number = {3},

pages = {616--626},

abstract = {Euglena sanguinea (Ehrenberg 1831) was one of the first green euglenoid species described in the literature. At first, the species aroused the interest of researchers mainly due to the blood-red color of its cells, which, as it later turned out, is not a constant feature. Complicated chloroplast morphology, labeled by Pringsheim as the "peculiar chromatophore system", made the correct identification of the species difficult, which is the reason why, throughout the 20th century, new species resembling E. sanguinea were continually being named due to a lack of suitable diagnostic features to distinguish E. sanguinea. Interest in E. sanguinea has returned in recent years, following findings that the species can produce ichthyotoxins. This was followed by the need to classify E. sanguinea correctly, which was achieved through the verification of morphological and molecular data for all species similar to E. sanguinea. As the result of the analysis, the number of species sharing some morphological similarities with E. sanguinea could be reduced from 12, as described in the literature, to four, with established epitypes and updated diagnostic descriptions. The most important diagnostic features included: the presence of mucocysts (i.e., whether they were visible before and/or after staining), the number of chloroplasts, the size of the double-sheathed pyrenoids, and the presence of the large paramylon grain in the vicinity of the stigma. Moreover, sequence analysis revealed the presence of unusually long SSU rDNA sequences in E. sanguinea. Previously, SSU rDNA sequences of such length were known to be present in primary osmotrophic euglenoids. textcopyright 2013 Phycological Society of America.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karnkowska-Ishikawa2012,

title = {Taxonomic revisions of morphologically similar species from two euglenoid genera: Euglena (E. granulata and E. velata) and Euglenaria (Eu. anabaena, Eu. caudata, and Eu. clavata)},

author = {Anna Karnkowska-Ishikawa and Rafał Milanowski and Richard E Triemer and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2012.01140.x},

doi = {10.1111/j.1529-8817.2012.01140.x},

issn = {00223646},

year  = {2012},

date = {2012-06-01},

journal = {Journal of Phycology},

volume = {48},

number = {3},

pages = {729--739},

abstract = {The establishment of epitypes (together with the emended diagnoses) for three species of Euglenaria Karnkowska, E. W. Linton et Kwiatowski [Eu. anabaena (Mainx) Karnkowska et E. W. Linton; Eu. caudata (Hu¨bner) Karnkowska et E. W. Linton; and Eu. clavata (Skuja) Karnkowska et E. W. Linton] and two species of Euglena Ehrenberg [E. granulata (Klebs) Schmitz and E. velata Klebs] was achieved due to literature studies, verification of morphological diagnostic features (cell size, cell shape, number of chloroplasts, the presence of mucocysts), as well as molecular characters (SSU rDNA). Now all these species are easy to identify and distinguish, despite their high morphological similarity, that is, spindleshaped (or cylindrically spindle-shaped) cells and parietal, lobed chloroplasts with a single pyrenoid, accompanied by bilateral paramylon caps located on both sides of the chloroplast. E. granulata is the only species in this group that has spherical mucocysts. E. velata is distinguished by the largest cells (90– 150 lm) and has the highest number of chloroplasts (textgreater30). Eu. anabaena has the fewest chloroplasts (usually 3–6), and its cells are always (whether the organism is swimming or not) spindle-shaped or cylindrically spindle-shaped, in contrast to the cells of Eu. clavata, which are club-shaped (clavate) while swimming and only after stopping change to resemble the shape of a spindle or a cylindrical spindle; Eu. clavata has numerous chloroplasts (15–20). Eu. caudata is characterized by asymmetrical spindleshaped (fusiform) cells, that is, with an elongated rear section and a shorter front section; the number of chloroplasts normally ranges from 7 to 15.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karnkowska-Ishikawa2011,

title = {The species Euglena deses (Euglenaceae) revisited: new morphological and molecular data},

author = {Anna Karnkowska-Ishikawa and Rafał Milanowski and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2011.00982.x},

doi = {10.1111/j.1529-8817.2011.00982.x},

issn = {00223646},

year  = {2011},

date = {2011-06-01},

journal = {Journal of Phycology},

volume = {47},

number = {3},

pages = {653--661},

abstract = {For this study, we have examined the literature and the morphological diversity, as well as analyzed the nuclear SSU rDNA sequences of two very common and cosmopolitan species formerly known as Euglena deses Ehrenb. and Euglena intermedia (G. A. Klebs) F. Schmitz. Our studies have shown that there is evidence for distinguishing only one species (E. deses). Here, we define new diagnostic features for E. deses, namely, periplast ornamentation (the presence of small papillae-discovered for the first time in this species) and the lateral location of the anterior canal opening, from which the flagellum emerges. We also designate the epitype and emend the diagnosis for E. deses. textcopyright 2011 Phycological Society of America.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Koperski2011,

title = {Searching for cryptic species in Erpobdella octoculata (L.) (Hirudinea: Clitellata): discordance between the results of genetic analysis and cross-breeding experiments},

author = {Paweł Koperski and Rafał Milanowski and Agnieszka Krzyk},

editor = {M Schilthuizen},

url = {http://dpc.uba.uva.nl/ctz/vol80/nr01/art04 https://brill.com/view/journals/ctoz/80/1/article-p85_4.xml},

doi = {10.1163/18759866-08001004},

issn = {1383-4517},

year  = {2011},

date = {2011-02-01},

journal = {Contributions to Zoology},

volume = {80},

number = {1},

pages = {85--94},

abstract = {The main aim of this study was to reveal reproduction barriers and potentially cryptic radiation within the very common and morphologically variable leech species - Erpobdella octoculata (L., 1758). The differences in reproductive success of the morphological forms were compared experimentally. The data based on the results of field sampling and analysis of ITS and COI sequences is also presented. The results of the analysis of DNA sequences clearly show lack of reproduction barriers between the analysed morphological forms. Subtle differences in DNA sequences between individuals, found with the use of the arbitrary primers method, seem to be related mainly to geographical distance between sub-populations. On the basis of these results, E. octoculata should be treated as one, valid species, in spite of its great morphological variability. However, experimentally confirmed differences in reproductive success of individuals belonging to morphologically divergent forms may be explained by the presence of reproductive barriers between them. Visible incongruity between the results of DNA sequences and the experimental results is not easy to explain - this question definitely needs further studies. Different percentages of morphological forms noted in field samples, suggests an adaptive value for divergent colour patterns in different habitats. Such differences may be a result of diverse mortality of individuals differing in colour dwelling on different bottom substrate, caused by predation by benthivorous fish.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Body2010,

title = {Did Trypanosomatid Parasites Contain a Eukaryotic Alga–Derived Plastid in Their Evolutionary Past?},

author = {Andrzej Bodył and Paweł Mackiewicz and Rafał Milanowski},

url = {http://www.ncbi.nlm.nih.gov/pubmed/20540605 http://www.bioone.org/doi/abs/10.1645/GE-1810.1},

doi = {10.1645/GE-1810.1},

issn = {0022-3395},

year  = {2010},

date = {2010-04-01},

journal = {Journal of Parasitology},

volume = {96},

number = {2},

pages = {465--475},

abstract = {The Trypanosomatidae is closely related to euglenids that harbor plastids acquired from a green alga via secondary endosymbiosis. This discovery led to the idea that trypanosomatid parasites contained a green alga-derived plastid in their evolutionary past, an evolutionary scenario that was criticized based on the rarity of plant/plastid/cyanobacterium-like genes in the completely sequenced genomes of Trypanosoma and Leishmania species. Because it is difficult to identify such genes, however, their apparent rarity does not preclude a previous plastid endosymbiosis in the Trypanosomatidae. The genome of the plastid-less apicomplexan Cryptosporidium parvum preserves only a handful of plant/plastid/cyanobacterium-like genes, suggesting massive loss of plastid genes after elimination of its plastid. Additional support for such wholesale gene loss comes from fucoxanthin-containing dinoflagellates. Trypanosomatid nuclear genomes contain cyanobacterium-, green plant-, and haptophyte alga-derived genes, suggesting that they could have possessed a plastid in their evolutionary past; however, these genes also could represent examples of more typical horizontal gene transfer that did not accompany a plastid endosymbiosis. Thus, the presence of host cell genes that were adapted for use in the plastid would be much stronger evidence for a past plastid endosymbiosis in the Trypanosomatidae. Good examples of such genes are those encoding superoxide dismutases (SODs). Trypanosomatid parasites possess 4 iron-containing SODs, with 2 of them, SODA and SODC, targeted to the mitochondrion. In contrast with SODAs with classical single-domain mitochondrial targeting signals, SODCs carry bipartite pre-sequences composed of a signal peptide, followed by a transit peptide. Interestingly, these N-terminal extensions show striking similarities in length, hydropathy profiles, amino acid composition, and targeting properties to pre-sequences of proteins targeted to eukaryotic alga-derived plastids of euglenids and dinoflagellates. In turn, phylogenetic analyses indicate that SODCs originated from a mitochondrion-targeted SOD via gene duplication and were inherited vertically in the trypanosomatid lineage. These data represent a new kind of evidence for a past plastid endosymbiosis in the Trypanosomatidae, but the nature of this plastid remains unclear. It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Delta 4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karnkowska-Ishikawa2010,

title = {Taxonomy of the Phacus oscillans (Euglenaceae) and its close relatives-balancing morphological and molecular features},

author = {Anna Karnkowska-Ishikawa and Rafał Milanowski and Jan Kwiatowski and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2009.00765.x},

doi = {10.1111/j.1529-8817.2009.00765.x},

issn = {00223646},

year  = {2010},

date = {2010-01-01},

journal = {Journal of Phycology},

volume = {46},

number = {1},

pages = {172--182},

abstract = {The establishment of epitypes (together with emended diagnoses) for seven species of Phacus Dujard. [Phacus oscillans G. A. Klebs, Phacus parvulus G. A. Klebs, Phacus pusillus Lemmerm., Phacus skujae Skvortzov, Phacus inflexus (Kisselew) Pochm., Phacus polytrophos Pochm., and Phacus smulkowskianus (Zakrys ´) Kusber] was achieved by literature studies, verification of morphological diagnostic features (cell size, cell shape), as well as molecular characters (SSU rDNA). The investigated Phacus species are mostly well distinguished morphologically, with an SSU rDNA interspecific sequence similarity of 95.1%–99.0% and an intraspecific sequence similarity of 99.0%–99.9%. Some of the phylogenetic relationships among the seven species have not been resolved, but the topology obtained indicates their assignment into two sister clades. The first clade is composed of two sister groups (P. parvulus and P. pusillus), while the second constitutes an assemblage of the remaining five species. The relationships between the clades remain unresolved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kosmala2009,

title = {Phylogeny and systematics of Euglena (Euglenaceae) species with axial, stellate chloroplasts based on morphological and molecular data-new taxa, emended diagnoses, and epitypifications},

author = {Sylwia Kosmala and Anna Karnkowska-Ishikawa and Rafał Milanowski and Jan Kwiatowski and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2009.00653.x},

doi = {10.1111/j.1529-8817.2009.00653.x},

issn = {00223646},

year  = {2009},

date = {2009-04-01},

journal = {Journal of Phycology},

volume = {45},

number = {2},

pages = {464--481},

abstract = {Morphological and molecular studies, as well as original literature reexamination, necessitate establishment of five Euglena species with a single axial, stellate chloroplast [Euglena viridis (O. F. Mu¨ller) Ehrenberg 1830, Euglena pseudoviridis Chadefaud 1937, Euglena stellata Mainx 1926, Euglena pseudostellata sp. nov., and Euglena cantabrica Pringsheim 1956], three species with two chloroplasts (Euglena geniculata Dujardin ex Schmitz 1884, Euglena chadefaudii Bourrelly 1951, and Euglena pseudochadefaudii sp. nov.), and one species with three chloroplasts (Euglena tristella Chu 1946). The primary morphological features, allowing distinction of the considered species are the presence and the shape of mucocysts, as well as the number of chloroplasts. Spherical mucocysts occur in E. cantabrica and E. geniculata, while spindle-shaped mucocysts are present in E. stellata, E. pseudostellata, E. chadefaudii, E. pseudochadefaudii, and E. tristella. No mucocysts are observed in E. viridis and E. pseudoviridis. Two new species (E. pseudochadefaudii sp. nov. and E. pseudostellata sp. nov.) differ from the respective species, E. chadefaudii and E. stellata, only at the molecular level. Molecular signatures and characteristic sequences are designated for nine distinguished species. Emended diagnoses for all and delimitation of epitypes for seven species (except E. viridis and E. tristella) are proposed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Koperski2008,

title = {Morphological , ecological and genetic divergence in po- pulations of Erpobdella octoculata (Hirudinea)},

author = {Paweł Koperski and Rafał Milanowski and Agnieszka Krzyk},

url = {https://www.zobodat.at/publikation_articles.php?id=190351},

year  = {2008},

date = {2008-01-01},

journal = {Lauterbornia},

volume = {65},

number = {1986},

pages = {63--67},

abstract = {Partial or complete reproduction barrier between co-habiting forms of the common leech Erpobdella octoculata and the cryptic radiation inside this taxa is searching for as a probable phenomenon. Different morphotypes of this polymorphic species were found in various types of freshwater environments in different proportions. The efficiency of reproduction between morphologically different specimens are visibly lower when compared with those between morphologically similar specimens. In spite of that, populations of E. octoculata seems to be genetically uniformed when COX1 and ITS regions are analyzed, which makes the hypothesis on existence of the reproduction barrier between the morphotypes less probable.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kosmala2007b,

title = {Morphological and molecular examination of relationships and epitype establishment of Phacus pleuronectes , Phacus orbicularis , and Phacus hamelii},

author = {Sylwia Kosmala and Magdalena Bereza and Rafał Milanowski and Jan Kwiatowski and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2007.00386.x},

doi = {10.1111/j.1529-8817.2007.00386.x},

issn = {00223646},

year  = {2007},

date = {2007-10-01},

journal = {Journal of Phycology},

volume = {43},

number = {5},

pages = {1071--1082},

abstract = {Verification of morphological diagnostic features and the establishment of three epitypes for three species of Phacus Dujardin—Phacus pleuronectes (O. F. Mu¨ll.) Dujardin, Phacus orbicularis Hu¨bner, and Phacus hamelii Allorge et Lefe`vre—was performed based on literature studies and analysis of morphological (cell shape, cell size, and periplast ornamentation) as well as molecular (18S rDNA) characters. Periplast ornamentation was recognized as a main diagnostic character, distinguishing P. orbicularis from P. pleuronectes and P. hamelii. Phacus orbicularis has struts running perpendicular to the longitudinal axis of the strips, while P. pleuronectes and P. hamelii do not. On the SSU rDNA tree, obtained by the Bayesian method, P. orbicularis, P. pleuronectes, and P. hamelii belong to three distinct clades. Some of the phylogenetic relationships are not resolved, but there are at least three Phacus species (P. hamatus, P. platyaulax, P. longicauda; for taxonomic authors, see Introduction) that are more closely related to P. orbicularis than is P. pleuronectes. Phacus hamelii is more closely related to P. ranula and the assemblage of several species of Phacus, which have small cells, than to P. orbicularis or P. pleuronectes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kosmala2007a,

title = {Phylogeny and systematics of the genus Monomorphina (Euglenaceae) based on morphological and molecular data},

author = {Sylwia Kosmala and Rafał Milanowski and Kamil Brzóska and Małgorzata Pękala and Jan Kwiatowski and Bożena Zakryś},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2006.00298.x},

doi = {10.1111/j.1529-8817.2006.00298.x},

issn = {00223646},

year  = {2007},

date = {2007-02-01},

journal = {Journal of Phycology},

volume = {43},

number = {1},

pages = {171--185},

abstract = {Morphological studies of 16 strains belonging to the genus Monomorphina revealed a single, parietal, orbicular chloroplast in their cells. The chloroplast has a tendency to be perforated and disintegrates in aging populations and thus may appear to be many chloroplasts under the light microscope. A single chloroplast in the cells of Cryptoglena skujae is also parietally located and highly perforated. It never forms a globular and closed structure, but is open from the side of the furrow, resembling the letter C. We have verified the Monomorphina pyrum group (M. pyrum–like) on the basis of phylogenetic analysis of SSU rDNA and morphological data. The strain CCAC 0093 (misidentified as M. reeuwykiana) diverges first on the SSU rDNA phylogenetic tree. The rest of the M. pyrum–like strains form a tight cluster, subdivided into several smaller ones. Because morphological differences between the M. pyrum– like strains (including the strain CCAC 0093) do not conform to the tree topology, we suggest that they all (except the strain CCAC 0093) belong to M. pyrum.We designate a new species, M. pseudopyrum, for the strain CCAC 0093, solely on the basis of molecular characters. We also suggest that M. reeuwykiana and similar species should stay in Phacus and Lepocinclis unless detailed molecular and morphological studies show otherwise. Emended diagnoses of the genera Monomorphina and Cryptoglena and the species M. aenigmatica are also proposed, as well as the delimitation of an epitype for M. pyrum, the type species for the genus Monomorphina.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Milanowski2006,

title = {Phylogeny of photosynthetic Euglenophytes based on combined chloroplast and cytoplasmic SSU rDNA sequence analysis},

author = {Rafał Milanowski and Sylwia Kosmala and Bożena Zakryś and Jan Kwiatowski},

url = {http://doi.wiley.com/10.1111/j.1529-8817.2006.00216.x},

doi = {10.1111/j.1529-8817.2006.00216.x},

issn = {0022-3646},

year  = {2006},

date = {2006-06-01},

journal = {Journal of Phycology},

volume = {42},

number = {3},

pages = {721--730},

abstract = {Eighteen new 16S rDNA and 16 new 18S rDNA sequences from 24 strains, representing 23 species of photoautotrophic euglenoids, were obtained in nearly their entire length. Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on separate data (39 sequences of 16S rDNA and 58 sequences of 18S rDNA), as well as on combined data sets (37 sequences). All methods of sequence analysis gave similar results in those cases in which the clades received substantial support. However, the combined data set produced several additional wellsupported clades, not encountered before in the analyses of green euglenoids. There are three main well-defined clades (A, B/C/D, and G) on trees from the combined data set. Clade G diverges first, while clades A and B/C/D form sister groups. Clade A consists of Euglena species sensu stricto and is divided into three sub-clades (A1, A2, and A3). Clade A3 (composed of E. deses and E. mutabilis) branches off first; then, two sister clades emerge: A1 (composed of E. viridis-like species) and A2 (consisting of E. agilis and E. gracilis species). Clade B/C/D consists of the Strombomonas, Trachelomonas, Cryptoglena, Monomorphina, and Colacium genera. Clade G comprises Phacus and Lepocinclis, as well as the Discoglena species of Euglena, with Discoglena branching off first, and then Phacus and Lepocinclis emerging as sister groups.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Komosińska2006,

title = {Some attempts to detect genetic differences between populations of small balsam (Impatiens parviflora DC.)},

author = {Emanuela Komosińska and Maciej Wódkiewicz and Ingeborga Jarzyna and Emilia Jarochowska and Rafał Milanowski and Katarzyna Chwedorzewska and Tomasz Wyszomirski},

url = {http://brc.amu.edu.pl/Some-attempts-to-detect-genetic-differences-between-populations-of-small-balsam-Impatiens,121607,0,2.html},

issn = {2080-945X},

year  = {2006},

date = {2006-01-01},

journal = {Biodiversity: Research and Conservation},

number = {3-4},

pages = {245--247},

abstract = {Invasive plants populations often originate from a few individuals, thus they may show very low genetic variability. On the other hand, differences between local populations can result from a rapid evolutionary change, which may play important role in the invasion process. We attempt to detect genetic differences between two Polish populations of small balsam, an annual plant highly invasive in Europe. Studies are conducted in parallel at two levels: morphological (by common garden experiments) and molecular (using AFLP method). AFLP shows no differences between the two populations, but the results obtained for some morphological measurements suggest that slight genetic differences between the two populations exist. Possibly they are too small to be detected through AFLP technique. Some of them can result from maternal effects; this is to be checked in further research.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/j.1529-8817.2005.00141.x,

title = {Phylogenetic and taxonomic position of Lepocinclis fusca comb. nov. (=Euglena fusca) (Euglenaceae): morphological and molecular justification},

author = {Sylwia Kosmala and Anna Karnkowska and Rafał Milanowski and Jan Kwiatowski and Bożena Zakryś},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.2005.00141.x},

doi = {https://doi.org/10.1111/j.1529-8817.2005.00141.x},

issn = {00223646},

year  = {2005},

date = {2005-01-01},

journal = {Journal of Phycology},

volume = {41},

number = {6},

pages = {1258-1267},

abstract = {We studied the morphological diversity and analyzed the small subunit rDNA sequences of two taxa formerly known as Euglena spirogyra Ehr. and Euglena fusca (Klebs) Lemmermann. Our studies confirmed that the two should have the rank of a species, namely Lepocinclis spirogyroides (Ehr.) Marin et Melkonian and Lepocinclis fusca (Klebs) Kosmala et Zakryś comb. nov. (Euglenophyceae). We are defining new diagnostic features for these species, namely the size and the shape of the cells and the shape of the papillae, as well as designating epitypes for them.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zakrys2004,

title = {Genetic variability of Euglena agilis (Euglenophyceae)},

author = {Bożena Zakryś and Joanna Empel and Rafał Milanowski and Robert Gromadka and Piotr Borsuk and Marta Kędzior and Jan Kwiatkowski},

url = {https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.2004.039},

doi = {10.5586/asbp.2004.039},

issn = {2083-9480},

year  = {2004},

date = {2004-01-01},

journal = {Acta Societatis Botanicorum Poloniae},

volume = {73},

number = {4},

pages = {305--309},

abstract = {The results of the internal transcribed spacer (ITS2) of extrachromosomal rDNA and the chloroplast SSU rDNA sequence analysis presented here confirmed elevated genetic polymorphism revealed earlier by RFLP and RAPD for seven clones of the cosmopolitan species - textlessemtextgreaterEuglena agilistextless/emtextgreater Carter. High diversity among these clonal strains was not reflected by morphological criteria, with the exception of the only one character - the ability of the cell in its non-motile dividing states (palmella) to produce mucus and form a slimy envelope. Evolutionary adaptation as formation of slimy envelope may be attributed to different survival strategy of the species by which it adapts to life in a highly variable environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zakrys2002,

title = {Two different species of Euglena, E. geniculata and E. myxocylindracea (Euglenophyceae), are virtually genetically and morphologically identical},

author = {Boz.ena Zakryś and Rafał Milanowski and Joanna Empel and Piotr Borsuk and Robert Gromadka and Jan Kwiatowski},

url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2002.02020.x/full http://doi.wiley.com/10.1046/j.1529-8817.2002.02020.x},

doi = {10.1046/j.1529-8817.2002.02020.x},

issn = {00223646},

year  = {2002},

date = {2002-12-01},

journal = {Journal of Phycology},

volume = {38},

number = {6},

pages = {1190--1199},

abstract = {We investigated the similarity of a single Euglena myxocylindracea strain, isolated originally by Bold and MacEntee, to several Euglena geniculata strains on both morphological and DNA levels. We found the three DNA stretches, consisting of fragments coding for the parts of cytoplasmic and chloroplast small subunit rRNA, and the internal transcribed spacer (ITS2) of cytoplasmic rDNA, with the combined length of 4332 nucleotides, are identical in E. myxocylindracea and E. geniculata , strain SAG 1224-4b. Morphological differences between E. myxocylindracea and any E. geniculata strain examined were well within the range of E. geniculata variability as well. The only difference behind the distinction of E. myxocylindracea from E. geniculata is the presence of the second chloroplast in the latter. However, we were able to induce the appearance of the second chloroplast in the cells of E. myxocylindracea and its disappearance in the cells of E. geniculata by changing the composition of the culture media. We therefore conclude that E. myxocylindracea Bold and MacEntee should be regarded as an environmental form of E. geniculata Dujardin. For the first time the morphology of E. geniculata chloroplasts was shown as revealed by confocal laser microscopy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Milanowski2001,

title = {Phylogenetic analysis of chloroplast small-subunit rRNA genes of the genus Euglena Ehrenberg.},

author = {Rafał Milanowski and B Zakryś and Jan Kwiatowski},

url = {http://www.ncbi.nlm.nih.gov/pubmed/11411697

http://ijs.sgmjournals.org/cgi/doi/10.1099/00207713-51-3-773

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-51-3-773},

doi = {10.1099/00207713-51-3-773},

issn = {1466-5026},

year  = {2001},

date = {2001-05-01},

journal = {International Journal of Systematic and Evolutionary Microbiology},

volume = {51},

number = {3},

pages = {773--781},

abstract = {Almost complete sequences of plastid SSU rDNA (16S rDNA) from 17 species belonging to the order Euglenales (sensu Nemeth, 1997; Shi et al., 1999) were determined and used to infer phylogenetic relationships between 10 species of Euglena, three of Phacus, and one of each of Colacium, Lepocinclis, Strombomonas, Trachelomonas and Eutreptia. The maximum-parsimony (MP), maximum-likelihood (ML) and distance analyses of the unambiguously aligned sequence fragments imply that the genus Euglena is not monophyletic. Parsimony and distance methods divide Euglenaceae into two sister groups. One comprises of representatives from the subgenera Phacus, Lepocinclis and Discoglena (sensu Zakryś, 1986), whereas the other includes members of Euglena and Calliglena subgenera (sensu Zakryś, 1986), intermixed with representatives of Colacium, Strombomonas and Trachelomonas. In all analyses subgenera Euglena--together with Euglena polymorpha (representative of the subgenus Calliglena)--and Discoglena--together with Phacus and Lepocinclis--form two well-defined clades. The data clearly indicate that a substantial revision of euglenoid systematics is very much required, nevertheless it must await while more information can be gathered, allowing resolution of outstanding relationships.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}