Biology Faculty Articles
Document Type
Article
Publication Date
4-15-2016
Publication Title
PLoS Genetics
ISSN
1553-7390
Volume
12
Issue/No.
4 e1005954
First Page
1
Last Page
35
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
NSUWorks Citation
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.
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
DOI
10.1371/journal.pgen.1005954
Comments
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.