Taksonomia, filogeneza i ewolucja klejnotek

@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{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{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{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{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{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}

}