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

Vij, S., Kuhl, H., Kuznetsova, I.S., Komissarov, A., Yurchenko, A.A., Van Heusden, P., Singh, S., Thevasagayam, N.M., Prakki, S.R.S., Purushothaman, K., Saju, J.M., Jiang, J., Mbandi, S.K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S.Y., Liew, W.C., Shen, X., Hon, L.S., Drake, J.P., Boitano, M., Hall, R., Chin, C-S, Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F.J., Vurture, G.W., Gopalapillai, G., Kumar Katneni, V., Noble, T.H., Scaria, V., Sivasubbu, S., Jerry, D.R., O'Brien, S.J., Schatz, M.C., Dalmay, T., Turner, S.W., Lok, S., Christoffels, A. and Orbán, L. (2016) Chromosomal-Level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12 (4). e1005954.

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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.

Item Type: Journal Article
Murdoch Affiliation(s): Centre for Comparative Genomics
Publisher: Public Library of Science
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