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

Shubha Vij (Lead Author), Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M. Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan ShenLawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán

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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.
Original languageEnglish
Article numbere1005954
JournalPLoS Genetics
Issue number4
Publication statusPublished - 15 Apr 2016

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