Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding

Vij, Shubha, Kuhl, Heiner, Kuznetsova, Inna S., Komissarov, Aleksey, Yurchenko, Andrey A., Van Heusden, Peter, Singh, Siddharth, Thevasagayam, Natascha M., Prakki, Sai Rama Sridatta, Purushothaman, Kathiresan, Saju, Jolly M., Jiang, Junhui, Mbandi, Stanley Kimbung, Jonas, Mario, Hin Yan Tong, Amy, Mwangi, Sarah, Lau, Doreen, Ngoh, Si Yan, Liew, Woei Chang, Shen, Xueyan, Hon, Lawrence S., Drake, James P., Boitano, Matthew, Hall, Richard, Chin, Chen-Shan, Lachumanan, Ramkumar, Korlach, Jonas, Trifonov, Vladimir, Kabilov, Marsel, Tupikin, Alexey, Green, Darrell, Moxon, Simon, Garvin, Tyler, Sedlazeck, Fritz J., Vurture, Gregory W., Gopalapillai, Gopikrishna, Kumar Katneni, Vinaya, Noble, Tansyn H., Scaria, Vinod, Sivasubbu, Sridhar, Jerry, Dean R., O'Brien, Stephen J., Schatz, Michael C., Dalmay, Tamás, Turner, Stephen W., Lok, Si, Christoffels, Alan, and Orbán, László (2016) Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12 (4). pp. 1-35.

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We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.

Item ID: 49283
Item Type: Article (Research - C1)
ISSN: 1553-7404
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This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Funders: National Research Foundation, Singapore (NRFS), National Research Foundation, South Africa, Siberian Branch of the Russian Academy of Sciences (SBRAS), Russian Ministry of Science (RMS), St. Petersburg State University (SPSU), Russian Foundation for Basic Research (RFBR), National Research Foundation (NRF), National Institute of Health (NIH), Cold Spring Harbor Laboratory (CSHL)
Projects and Grants: NRFS-CRP7-2010-01, SBRAS no. 137, RMS Mega-grant no. 11.G34.31.0068, SPSU Research grant IAS, RFBR no. 14-14-00275, NRF DBI-1350041, NRF IOS-1237880, NIH R01-HG006677, CSHL 5T32GM065094
Date Deposited: 09 Jun 2017 04:14
FoR Codes: 31 BIOLOGICAL SCIENCES > 3105 Genetics > 310509 Genomics @ 100%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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