Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

• DOI: 10.1371/journal.pgen.1005954
• Publication Date: 2016-04-15T17:36:13Z
• Authors: Shubha Vij; Heiner Kuhl; Inna S. Kuznetsova; Aleksey Komissarov; Andrey A. Yurchenko; Peter Van Heusden; Siddharth Singh; Natascha M. Theva...; Sai Rama Sridatta...; Kathiresan Purush...; Jolly M. Saju; Junhui Jiang; Stanley Kimbung M...; 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 Gopal...; Vinaya Kumar Katneni; Tansyn H. Noble; Vinod Scaria; Sridhar Sivasubbu; Dean R. Jerry; Stephen J. O'Brien; Michael C. Schatz; Tamás Dalmay; Stephen W. Turner; Si Lok; Alan Christoffels; László Orbán
• Keywords: Synteny; Sequence assembly

We report here the ~670 Mb genome assembly of Asian seabass (Lates calcarifer), a tropical marine teleost. used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive chromosome-level contig N50 size over 1 scaffold 25 that span ~90% genome. The population structure L. calcarifer complex was analyzed re-sequencing 61 individuals representing various regions across species’ native range. SNP analyses identified high levels diversity confirmed earlier indications stratification comprising three clades signs admixture apparent in South-East population. quality far exceeds any other species, will serve as new standard for genomics.