July 19, 2019  |  

Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding.

Authors: Vij, Shubha and Kuhl, Heiner and Kuznetsova, Inna S and Komissarov, Aleksey and Yurchenko, Andrey A and Van Heusden, Peter and Singh, Siddharth and Thevasagayam, Natascha M and Prakki, Sai Rama Sridatta and Purushothaman, Kathiresan and Saju, Jolly M and Jiang, Junhui and Mbandi, Stanley Kimbung and Jonas, Mario and Hin Yan Tong, Amy and Mwangi, Sarah and Lau, Doreen and Ngoh, Si Yan and Liew, Woei Chang and Shen, Xueyan and Hon, Lawrence S and Drake, James P and Boitano, Matthew and Hall, Richard and Chin, Chen-Shan and Lachumanan, Ramkumar and Korlach, Jonas and Trifonov, Vladimir and Kabilov, Marsel and Tupikin, Alexey and Green, Darrell and Moxon, Simon and Garvin, Tyler and Sedlazeck, Fritz J and Vurture, Gregory W and Gopalapillai, Gopikrishna and Kumar Katneni, Vinaya and Noble, Tansyn H and Scaria, Vinod and Sivasubbu, Sridhar and Jerry, Dean R and O'Brien, Stephen J and Schatz, Michael C and Dalmay, Tamás and Turner, Stephen W and Lok, Si and Christoffels, Alan and Orbán, László

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.

Journal: PLoS genetics
DOI: 10.1371/journal.pgen.1005954
Year: 2016

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