Binning tetraploid genomes into four subgenomes using BUSCO genes.
<p><b>(A)</b> Using a greedy algorithm, we iterated through contigs from largest to smallest, appending a contig to a haplotypic subgenome if the duplication contributed by that contig does not exceed a specified threshold (<i>x</i> axes in the figure). Single-copy BUSC...
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| مؤلفون آخرون: | , , , , , , , , , , , |
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2025
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| _version_ | 1852015643633647616 |
|---|---|
| author | Amjad Khalaf (22470183) |
| author2 | Chenxi Zhou (369944) Claudia C. Weber (22470186) Emmelien Vancaester (3631018) Ying Sims (12076085) Alex Makunin (10874350) Thomas C. Mathers (3262077) Dominic E. Absolon (21653669) Jonathan M. D. Wood (17797713) Shane A. McCarthy (3170157) Kamil S. Jaron (12153067) Mark Blaxter (50235) Mara K. N. Lawniczak (7832150) |
| author2_role | author author author author author author author author author author author author |
| author_facet | Amjad Khalaf (22470183) Chenxi Zhou (369944) Claudia C. Weber (22470186) Emmelien Vancaester (3631018) Ying Sims (12076085) Alex Makunin (10874350) Thomas C. Mathers (3262077) Dominic E. Absolon (21653669) Jonathan M. D. Wood (17797713) Shane A. McCarthy (3170157) Kamil S. Jaron (12153067) Mark Blaxter (50235) Mara K. N. Lawniczak (7832150) |
| author_role | author |
| dc.creator.none.fl_str_mv | Amjad Khalaf (22470183) Chenxi Zhou (369944) Claudia C. Weber (22470186) Emmelien Vancaester (3631018) Ying Sims (12076085) Alex Makunin (10874350) Thomas C. Mathers (3262077) Dominic E. Absolon (21653669) Jonathan M. D. Wood (17797713) Shane A. McCarthy (3170157) Kamil S. Jaron (12153067) Mark Blaxter (50235) Mara K. N. Lawniczak (7832150) |
| dc.date.none.fl_str_mv | 2025-10-21T17:40:44Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pbio.3003446.g008 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Binning_tetraploid_genomes_into_four_subgenomes_using_BUSCO_genes_/30410045 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Microbiology Genetics Evolutionary Biology Ecology Marine Biology Infectious Diseases Biological Sciences not elsewhere classified quality genome assemblies infected arthropod hosts growing public health chromatin conformation capture obligately intracellular parasites different microsporidian groups xlink "> microsporidia create reference genomes tetraploid genome haplotypes results provide evidence partial microsporidian genomes microsporidia </ p two diploid units microsporidian parasites microsporidian lifecycle tetraploid genomes homeologous genomes complete genomes striking tolerance sexual reproduction sexual cycle segmental duplications scale rearrangements many aspects likely recombine likely organized life project help answer evolution unexplored economic importance diploid lineages dikaryotic cells data indicated darwin tree characterized 14 also observed |
| dc.title.none.fl_str_mv | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p><b>(A)</b> Using a greedy algorithm, we iterated through contigs from largest to smallest, appending a contig to a haplotypic subgenome if the duplication contributed by that contig does not exceed a specified threshold (<i>x</i> axes in the figure). Single-copy BUSCO gene completeness is marked by circles and multi-copy BUSCO gene completeness is marked by crosses. A red dashed line denotes the BUSCO completeness score of the unbinned assembly. For <b>(B)</b> idChiSpeb1.µ and <b>(C)</b> ilAceEphe1.µ, we plotted the largest 10 contigs in subgenome 1 with their BUSCO genes, and coloured these genes in the other subgenomes by their positions in subgenome 1. The BUSCO annotations underlying this figure can be found in File Collection 5 at <a href="https://doi.org/10.5281/zenodo.17251512" target="_blank">https://doi.org/10.5281/zenodo.17251512</a>. The figure was generated using gerbil (<a href="https://github.com/Amjad-Khalaf/gerbil" target="_blank">https://github.com/Amjad-Khalaf/gerbil</a>), and manually annotated using <a href="https://inkscape.org/" target="_blank">InkScape</a> (version 1.2.2).</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_fbf7cae19dce0a0e02a7a4e0870e88be |
| identifier_str_mv | 10.1371/journal.pbio.3003446.g008 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30410045 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Binning tetraploid genomes into four subgenomes using BUSCO genes.Amjad Khalaf (22470183)Chenxi Zhou (369944)Claudia C. Weber (22470186)Emmelien Vancaester (3631018)Ying Sims (12076085)Alex Makunin (10874350)Thomas C. Mathers (3262077)Dominic E. Absolon (21653669)Jonathan M. D. Wood (17797713)Shane A. McCarthy (3170157)Kamil S. Jaron (12153067)Mark Blaxter (50235)Mara K. N. Lawniczak (7832150)MicrobiologyGeneticsEvolutionary BiologyEcologyMarine BiologyInfectious DiseasesBiological Sciences not elsewhere classifiedquality genome assembliesinfected arthropod hostsgrowing public healthchromatin conformation captureobligately intracellular parasitesdifferent microsporidian groupsxlink "> microsporidiacreate reference genomestetraploid genome haplotypesresults provide evidencepartial microsporidian genomesmicrosporidia </ ptwo diploid unitsmicrosporidian parasitesmicrosporidian lifecycletetraploid genomeshomeologous genomescomplete genomesstriking tolerancesexual reproductionsexual cyclesegmental duplicationsscale rearrangementsmany aspectslikely recombinelikely organizedlife projecthelp answerevolution unexploredeconomic importancediploid lineagesdikaryotic cellsdata indicateddarwin treecharacterized 14also observed<p><b>(A)</b> Using a greedy algorithm, we iterated through contigs from largest to smallest, appending a contig to a haplotypic subgenome if the duplication contributed by that contig does not exceed a specified threshold (<i>x</i> axes in the figure). Single-copy BUSCO gene completeness is marked by circles and multi-copy BUSCO gene completeness is marked by crosses. A red dashed line denotes the BUSCO completeness score of the unbinned assembly. For <b>(B)</b> idChiSpeb1.µ and <b>(C)</b> ilAceEphe1.µ, we plotted the largest 10 contigs in subgenome 1 with their BUSCO genes, and coloured these genes in the other subgenomes by their positions in subgenome 1. The BUSCO annotations underlying this figure can be found in File Collection 5 at <a href="https://doi.org/10.5281/zenodo.17251512" target="_blank">https://doi.org/10.5281/zenodo.17251512</a>. The figure was generated using gerbil (<a href="https://github.com/Amjad-Khalaf/gerbil" target="_blank">https://github.com/Amjad-Khalaf/gerbil</a>), and manually annotated using <a href="https://inkscape.org/" target="_blank">InkScape</a> (version 1.2.2).</p>2025-10-21T17:40:44ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pbio.3003446.g008https://figshare.com/articles/figure/Binning_tetraploid_genomes_into_four_subgenomes_using_BUSCO_genes_/30410045CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/304100452025-10-21T17:40:44Z |
| spellingShingle | Binning tetraploid genomes into four subgenomes using BUSCO genes. Amjad Khalaf (22470183) Microbiology Genetics Evolutionary Biology Ecology Marine Biology Infectious Diseases Biological Sciences not elsewhere classified quality genome assemblies infected arthropod hosts growing public health chromatin conformation capture obligately intracellular parasites different microsporidian groups xlink "> microsporidia create reference genomes tetraploid genome haplotypes results provide evidence partial microsporidian genomes microsporidia </ p two diploid units microsporidian parasites microsporidian lifecycle tetraploid genomes homeologous genomes complete genomes striking tolerance sexual reproduction sexual cycle segmental duplications scale rearrangements many aspects likely recombine likely organized life project help answer evolution unexplored economic importance diploid lineages dikaryotic cells data indicated darwin tree characterized 14 also observed |
| status_str | publishedVersion |
| title | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| title_full | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| title_fullStr | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| title_full_unstemmed | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| title_short | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| title_sort | Binning tetraploid genomes into four subgenomes using BUSCO genes. |
| topic | Microbiology Genetics Evolutionary Biology Ecology Marine Biology Infectious Diseases Biological Sciences not elsewhere classified quality genome assemblies infected arthropod hosts growing public health chromatin conformation capture obligately intracellular parasites different microsporidian groups xlink "> microsporidia create reference genomes tetraploid genome haplotypes results provide evidence partial microsporidian genomes microsporidia </ p two diploid units microsporidian parasites microsporidian lifecycle tetraploid genomes homeologous genomes complete genomes striking tolerance sexual reproduction sexual cycle segmental duplications scale rearrangements many aspects likely recombine likely organized life project help answer evolution unexplored economic importance diploid lineages dikaryotic cells data indicated darwin tree characterized 14 also observed |