A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

Autor:	Bukhman YV; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Morin PA; Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA., Meyer S; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Chu LF; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA.; Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada., Jacobsen JK; V.E. Enterprises, Arcata, CA, USA., Antosiewicz-Bourget J; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Mamott D; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Gonzales M; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Argus C; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Bolin J; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Berres ME; University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA., Fedrigo O; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA., Steill J; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Swanson SA; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Jiang P; Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA.; Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.; Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA., Rhie A; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA., Formenti G; Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA., Phillippy AM; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA., Harris RS; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA., Wood JMD; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Howe K; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Kirilenko BM; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.; Senckenberg Research Institute, 60325 Frankfurt, Germany.; Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany., Munegowda C; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.; Senckenberg Research Institute, 60325 Frankfurt, Germany.; Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany., Hiller M; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.; Senckenberg Research Institute, 60325 Frankfurt, Germany.; Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany., Jain A; Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA., Kihara D; Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA., Johnston JS; Department of Entomology, Texas A&M University, College Station, TX 77843, USA., Ionkov A; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Raja K; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA., Toh H; Neuroscience Research Institute, University of California, Santa Barbara, CA, USA., Lang A; Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA., Wolf M; Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany.; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany., Jarvis ED; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.; Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA., Thomson JA; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA.; Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA.; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA., Chaisson MJP; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA., Stewart R; Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA.
Jazyk:	angličtina
Zdroj:	Molecular biology and evolution [Mol Biol Evol] 2024 Mar 01; Vol. 41 (3).
DOI:	10.1093/molbev/msae036
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu