A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography
Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fas...
Published in: | Molecular Biology and Evolution |
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Language: | English |
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Oxford University Press (OUP)
2024
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Online Access: | http://dx.doi.org/10.1093/molbev/msae036 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msae036/56719079/msae036.pdf https://academic.oup.com/mbe/article-pdf/41/3/msae036/56902793/msae036.pdf |
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croxfordunivpr:10.1093/molbev/msae036 2024-09-30T14:32:43+00:00 A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography Bukhman, Yury V Morin, Phillip A Meyer, Susanne Chu, Li-Fang Jacobsen, Jeff K Antosiewicz-Bourget, Jessica Mamott, Daniel Gonzales, Maylie Argus, Cara Bolin, Jennifer Berres, Mark E Fedrigo, Olivier Steill, John Swanson, Scott A Jiang, Peng Rhie, Arang Formenti, Giulio Phillippy, Adam M Harris, Robert S Wood, Jonathan M D Howe, Kerstin Kirilenko, Bogdan M Munegowda, Chetan Hiller, Michael Jain, Aashish Kihara, Daisuke Johnston, J Spencer Ionkov, Alexander Raja, Kalpana Toh, Huishi Lang, Aimee Wolf, Magnus Jarvis, Erich D Thomson, James A Chaisson, Mark J P Stewart, Ron Gaut, Brandon Morgridge Institute for Research Marv Conney NSF CAREER LOEWE-Centre for Translational Biodiversity Genomics Hessen State Ministry of Higher Education, Research and the Arts Intramural Research Program of the National Human Genome Research Institute National Institutes of Health Howard Hughes Medical Institute Rockefeller University 2024 http://dx.doi.org/10.1093/molbev/msae036 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msae036/56719079/msae036.pdf https://academic.oup.com/mbe/article-pdf/41/3/msae036/56902793/msae036.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ Molecular Biology and Evolution volume 41, issue 3 ISSN 0737-4038 1537-1719 journal-article 2024 croxfordunivpr https://doi.org/10.1093/molbev/msae036 2024-09-17T04:30:46Z Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research. Article in Journal/Newspaper Balaenoptera musculus Blue whale Oxford University Press Pacific Molecular Biology and Evolution 41 3 |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research. |
author2 |
Gaut, Brandon Morgridge Institute for Research Marv Conney NSF CAREER LOEWE-Centre for Translational Biodiversity Genomics Hessen State Ministry of Higher Education, Research and the Arts Intramural Research Program of the National Human Genome Research Institute National Institutes of Health Howard Hughes Medical Institute Rockefeller University |
format |
Article in Journal/Newspaper |
author |
Bukhman, Yury V Morin, Phillip A Meyer, Susanne Chu, Li-Fang Jacobsen, Jeff K Antosiewicz-Bourget, Jessica Mamott, Daniel Gonzales, Maylie Argus, Cara Bolin, Jennifer Berres, Mark E Fedrigo, Olivier Steill, John Swanson, Scott A Jiang, Peng Rhie, Arang Formenti, Giulio Phillippy, Adam M Harris, Robert S Wood, Jonathan M D Howe, Kerstin Kirilenko, Bogdan M Munegowda, Chetan Hiller, Michael Jain, Aashish Kihara, Daisuke Johnston, J Spencer Ionkov, Alexander Raja, Kalpana Toh, Huishi Lang, Aimee Wolf, Magnus Jarvis, Erich D Thomson, James A Chaisson, Mark J P Stewart, Ron |
spellingShingle |
Bukhman, Yury V Morin, Phillip A Meyer, Susanne Chu, Li-Fang Jacobsen, Jeff K Antosiewicz-Bourget, Jessica Mamott, Daniel Gonzales, Maylie Argus, Cara Bolin, Jennifer Berres, Mark E Fedrigo, Olivier Steill, John Swanson, Scott A Jiang, Peng Rhie, Arang Formenti, Giulio Phillippy, Adam M Harris, Robert S Wood, Jonathan M D Howe, Kerstin Kirilenko, Bogdan M Munegowda, Chetan Hiller, Michael Jain, Aashish Kihara, Daisuke Johnston, J Spencer Ionkov, Alexander Raja, Kalpana Toh, Huishi Lang, Aimee Wolf, Magnus Jarvis, Erich D Thomson, James A Chaisson, Mark J P Stewart, Ron A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
author_facet |
Bukhman, Yury V Morin, Phillip A Meyer, Susanne Chu, Li-Fang Jacobsen, Jeff K Antosiewicz-Bourget, Jessica Mamott, Daniel Gonzales, Maylie Argus, Cara Bolin, Jennifer Berres, Mark E Fedrigo, Olivier Steill, John Swanson, Scott A Jiang, Peng Rhie, Arang Formenti, Giulio Phillippy, Adam M Harris, Robert S Wood, Jonathan M D Howe, Kerstin Kirilenko, Bogdan M Munegowda, Chetan Hiller, Michael Jain, Aashish Kihara, Daisuke Johnston, J Spencer Ionkov, Alexander Raja, Kalpana Toh, Huishi Lang, Aimee Wolf, Magnus Jarvis, Erich D Thomson, James A Chaisson, Mark J P Stewart, Ron |
author_sort |
Bukhman, Yury V |
title |
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
title_short |
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
title_full |
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
title_fullStr |
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
title_full_unstemmed |
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography |
title_sort |
high-quality blue whale genome, segmental duplications, and historical demography |
publisher |
Oxford University Press (OUP) |
publishDate |
2024 |
url |
http://dx.doi.org/10.1093/molbev/msae036 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msae036/56719079/msae036.pdf https://academic.oup.com/mbe/article-pdf/41/3/msae036/56902793/msae036.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Balaenoptera musculus Blue whale |
genre_facet |
Balaenoptera musculus Blue whale |
op_source |
Molecular Biology and Evolution volume 41, issue 3 ISSN 0737-4038 1537-1719 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/molbev/msae036 |
container_title |
Molecular Biology and Evolution |
container_volume |
41 |
container_issue |
3 |
_version_ |
1811636785511399424 |