mgr Paweł Hałakuc

@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{nokey,

title = {Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: Insights from metabarcoding and machine learning},

author = {Michał Karlicki and Anna Bednarska and Paweł Hałakuc and Kacper Maciszewski and Anna Karnkowska},

doi = {10.1093/femsec/fiae104},

year  = {2024},

date = {2024-07-22},

urldate = {2024-07-22},

journal = {FEMS Microbiology Ecology},

volume = {100},

issue = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Peona2024,

title = {Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective},

author = {Valentina Peona and Jacopo Martelossi and Dareen Almojil and Julia Bocharkina and Ioana Brännström and Max Brown and Alice Cang and Tomàs Carrasco-Valenzuela and Jon DeVries and Meredith Doellman and Daniel Elsner and Pamela Espíndola-Hernández and Guillermo Friis Montoya and Bence Gaspar and Danijela Zagorski and Paweł Hałakuc and Beti Ivanovska and Christopher Laumer and Robert Lehmann and Ljudevit Luka Boštjančić and Rahia Mashoodh and Sofia Mazzoleni and Alice Mouton and Maria Anna Nilsson and Yifan Pei and Giacomo Potente and Panagiotis Provataris and José Ramón Pardos-Blas and Ravindra Raut and Tomasa Sbaffi and Florian Schwarz and Jessica Stapley and Lewis Stevens and Nusrat Sultana and Radka Symonova and Mohadeseh S. Tahami and Alice Urzì and Heidi Yang and Abdullah Yusuf and Carlo Pecoraro and Alexander Suh},

doi = {10.1186/s13100-024-00319-8},

issn = {1759-8753},

year  = {2024},

date = {2024-05-06},

urldate = {2024-12-00},

journal = {Mobile DNA},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:sec>

                <jats:title>Background</jats:title>

                <jats:p>The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Results</jats:title>

                <jats:p>Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.</jats:p>

              </jats:sec><jats:sec>

                <jats:title>Conclusions</jats:title>

                <jats:p>The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.</jats:p>

              </jats:sec>},

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{10.1371/journal.pgen.1011050,

title = {Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria},

author = {Lukáš V. F. Novák and Sebastian C. Treitli and Jan Pyrih and Paweł Hałakuc and Shweta V. Pipaliya and Vojtěch Vacek and Ondřej Brzoň and Petr Soukal and Laura Eme and Joel B. Dacks and Anna Karnkowska and Marek Eliáš and Vladimír Hampl},

url = {https://doi.org/10.1371/journal.pgen.1011050},

doi = {10.1371/journal.pgen.1011050},

year  = {2023},

date = {2023-12-07},

urldate = {2023-12-07},

journal = {PLOS Genetics},

volume = {19},

number = {12},

pages = {1-30},

publisher = {Public Library of Science},

abstract = {The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.},

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{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{mbs:/content/journal/mgen/10.1099/mgen.0.000745,

title = {High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis},

author = {Sebastian Cristian Treitli and Priscila Peña-Diaz and Paweł Hałakuc and Anna Karnkowska and Vladimír Hampl},

url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000745},

doi = {https://doi.org/10.1099/mgen.0.000745},

issn = {2057-5858},

year  = {2021},

date = {2021-12-24},

journal = {Microbial Genomics},

volume = {7},

number = {12},

pages = {000745},

publisher = {Microbiology Society},

abstract = {Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.},

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}

}