Biology Faculty Articles
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
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.
GenBank accession #: LLXD00000000; Singapore Competitive Research Program # NRF-CRP7-2010-01; Russian Academy of Sciences grant #: SB RAS no. 137; Russian Ministry of Science megagrant #: 11.G34.31.0068; St. Petersburg State University grant #: IAS 126.96.36.1994; Russian Foundation for Basic Research grant #: RFBR 14-14-00275; National Science Foundation award #s: DBI-1350041, IOS-1237880; National Institute of Health award #: R01-HG006677; Cold Spring Harbor Laboratory training grant #: 5T32GM065094
Vij, Shubha; Heiner Kuhl; Inna S. Kuznetsova; Aleksey Komissarov; Andrey A. Yurchenko; Peter Van Heusden; Siddharth Singh; Natascha May 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 Shen; Lawrence 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; and Laszlo Orban. 2016. "Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding." PLoS Genetics 12, (4 e1005954): 1-35. doi:10.1371/journal.pgen.1005954.
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