Journal article
Chromosomal-Level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding
PLoS Genetics, Vol.12(4), e1005954
2016
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.
Details
- Title
- Chromosomal-Level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding
- Authors/Creators
- S. Vij (Author/Creator)H. Kuhl (Author/Creator)I.S. Kuznetsova (Author/Creator)A. Komissarov (Author/Creator)A.A. Yurchenko (Author/Creator)P. Van Heusden (Author/Creator)S. Singh (Author/Creator)N.M. Thevasagayam (Author/Creator)S.R.S. Prakki (Author/Creator)K. Purushothaman (Author/Creator)J.M. Saju (Author/Creator)J. Jiang (Author/Creator)S.K. Mbandi (Author/Creator)M. Jonas (Author/Creator)A. Hin Yan Tong (Author/Creator)S. Mwangi (Author/Creator)D. Lau (Author/Creator)S.Y. Ngoh (Author/Creator)W.C. Liew (Author/Creator)X. Shen (Author/Creator)L.S. Hon (Author/Creator)J.P. Drake (Author/Creator)M. Boitano (Author/Creator)R. Hall (Author/Creator)C-S Chin (Author/Creator)R. Lachumanan (Author/Creator)J. Korlach (Author/Creator)V. Trifonov (Author/Creator)M. Kabilov (Author/Creator)A. Tupikin (Author/Creator)D. Green (Author/Creator)S. Moxon (Author/Creator)T. Garvin (Author/Creator)F.J. Sedlazeck (Author/Creator)G.W. Vurture (Author/Creator)G. Gopalapillai (Author/Creator)V. Kumar Katneni (Author/Creator)T.H. Noble (Author/Creator)V. Scaria (Author/Creator)S. Sivasubbu (Author/Creator)D.R. Jerry (Author/Creator)S.J. O'Brien (Author/Creator)M.C. Schatz (Author/Creator)T. Dalmay (Author/Creator)S.W. Turner (Author/Creator)S. Lok (Author/Creator)A. Christoffels (Author/Creator)L. Orbán (Author/Creator)
- Publication Details
- PLoS Genetics, Vol.12(4), e1005954
- Publisher
- Public Library of Science
- Identifiers
- 991005543976507891
- Murdoch Affiliation
- Centre for Comparative Genomics
- Language
- English
- Resource Type
- Journal article
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