Article
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
PLoS Genetics
Document Type
Article
Publication Date
4-15-2016
Disciplines
Abstract
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.
Additional Comments
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 1.37.153.2014; 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
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
DOI
10.1371/journal.pgen.1005954
Citation Information
Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, et al.. "Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding" PLoS Genetics Vol. 12 Iss. 4 e1005954 (2016) p. 1 - 35 ISSN: 1553-7390 Available at: http://works.bepress.com/stephen-obrien/672/
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