Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved]
Mollusca is the second most species-rich phylum and includes animals as disparate as octopuses, clams, and chitons. Dozens of molluscan genomes are available, but only one representative of the subphylum Aculifera, the sister taxon to all other molluscs, has been sequenced to date, hindering compara...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2022-05-01
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| Online Access: | https://f1000research.com/articles/11-555/v1 |
| _version_ | 1797996378410975232 |
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| author | Kevin M. Kocot Meghan K. Yap-Chiongco Nina T. Mikkelsen Rebecca M. Varney |
| author_facet | Kevin M. Kocot Meghan K. Yap-Chiongco Nina T. Mikkelsen Rebecca M. Varney |
| author_sort | Kevin M. Kocot |
| collection | DOAJ |
| description | Mollusca is the second most species-rich phylum and includes animals as disparate as octopuses, clams, and chitons. Dozens of molluscan genomes are available, but only one representative of the subphylum Aculifera, the sister taxon to all other molluscs, has been sequenced to date, hindering comparative and evolutionary studies. To facilitate evolutionary studies across Mollusca, we sequenced the genome of a second aculiferan mollusc, the lepidopleurid chiton Hanleya hanleyi (Bean 1844), using a hybrid approach combining Oxford Nanopore and Illumina reads. After purging redundant haplotigs and removing contamination from this 1.3% heterozygous genome, we produced a 2.5 Gbp haploid assembly (>4X the size of the other chiton genome sequenced to date) with an N50 of 65.0 Kbp. Despite a fragmented assembly, the genome is rather complete (92.0% of BUSCOs detected; 79.4% complete plus 12.6% fragmented). Remarkably, the genome has the highest repeat content of any molluscan genome reported to date (>66%). Our gene annotation pipeline predicted 69,284 gene models (92.9% of BUSCOs detected; 81.8% complete plus 11.1% fragmented) of which 35,362 were supported by transcriptome and/or protein evidence. Phylogenomic analysis recovered Polyplacophora sister to all other sampled molluscs with maximal support. The Hanleya genome will be a valuable resource for studies of molluscan biology with diverse potential applications ranging from evolutionary and comparative genomics to molecular ecology. |
| first_indexed | 2024-04-11T10:16:33Z |
| format | Article |
| id | doaj.art-c3ef490d7013467781bce50386039ad9 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-11T10:16:33Z |
| publishDate | 2022-05-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-c3ef490d7013467781bce50386039ad92022-12-22T04:29:56ZengF1000 Research LtdF1000Research2046-14022022-05-0111133601Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved]Kevin M. Kocot0Meghan K. Yap-Chiongco1Nina T. Mikkelsen2https://orcid.org/0000-0002-6222-5227Rebecca M. Varney3Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USADepartment of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USAUniversity Museum of Bergen, Univeristy of Bergen, Bergen, 5020, NorwayEcology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USAMollusca is the second most species-rich phylum and includes animals as disparate as octopuses, clams, and chitons. Dozens of molluscan genomes are available, but only one representative of the subphylum Aculifera, the sister taxon to all other molluscs, has been sequenced to date, hindering comparative and evolutionary studies. To facilitate evolutionary studies across Mollusca, we sequenced the genome of a second aculiferan mollusc, the lepidopleurid chiton Hanleya hanleyi (Bean 1844), using a hybrid approach combining Oxford Nanopore and Illumina reads. After purging redundant haplotigs and removing contamination from this 1.3% heterozygous genome, we produced a 2.5 Gbp haploid assembly (>4X the size of the other chiton genome sequenced to date) with an N50 of 65.0 Kbp. Despite a fragmented assembly, the genome is rather complete (92.0% of BUSCOs detected; 79.4% complete plus 12.6% fragmented). Remarkably, the genome has the highest repeat content of any molluscan genome reported to date (>66%). Our gene annotation pipeline predicted 69,284 gene models (92.9% of BUSCOs detected; 81.8% complete plus 11.1% fragmented) of which 35,362 were supported by transcriptome and/or protein evidence. Phylogenomic analysis recovered Polyplacophora sister to all other sampled molluscs with maximal support. The Hanleya genome will be a valuable resource for studies of molluscan biology with diverse potential applications ranging from evolutionary and comparative genomics to molecular ecology.https://f1000research.com/articles/11-555/v1Aculifera Lepidopleurida genome repetitive DNAeng |
| spellingShingle | Kevin M. Kocot Meghan K. Yap-Chiongco Nina T. Mikkelsen Rebecca M. Varney Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] F1000Research Aculifera Lepidopleurida genome repetitive DNA eng |
| title | Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] |
| title_full | Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] |
| title_fullStr | Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] |
| title_full_unstemmed | Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] |
| title_short | Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora) [version 1; peer review: 2 approved] |
| title_sort | genome of the lepidopleurid chiton hanleya hanleyi mollusca polyplacophora version 1 peer review 2 approved |
| topic | Aculifera Lepidopleurida genome repetitive DNA eng |
| url | https://f1000research.com/articles/11-555/v1 |
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