Browsing by Author "Vij, Shubha"

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    Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
    (Public Library of Science, 2016) Vij, Shubha; Van Heusden, Peter; Christoffels, Alan; Mbandi, Stanley K.; Mwangi, Sarah
    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.