Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
| Autor: | Shubha Vij, Heiner Kuhl, Inna S Kuznetsova, Aleksey Komissarov, Andrey A Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M Saju, Junhui Jiang, Stanley Kimbung Mbandi, 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 Gopalapillai, 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 |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: | |
| Zdroj: | PLoS Genetics, Vol 12, Iss 4, p e1005954 (2016) |
| Druh dokumentu: | article |
| ISSN: | 1553-7390 1553-7404 |
| DOI: | 10.1371/journal.pgen.1005954 |
| Popis: | 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. |
| Databáze: | Directory of Open Access Journals |
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