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

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...

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Published in:PLoS genetics 2016-04, Vol.12 (4), p.e1005954-e1005954
Main Authors: Vij, Shubha, Kuhl, Heiner, Kuznetsova, Inna S, Komissarov, Aleksey, Yurchenko, Andrey A, Van Heusden, Peter, Singh, Siddharth, Thevasagayam, Natascha M, Prakki, Sai Rama Sridatta, Purushothaman, Kathiresan, Saju, Jolly M, Jiang, Junhui, Mbandi, Stanley Kimbung, Jonas, Mario, Hin Yan Tong, Amy, Mwangi, Sarah, Lau, Doreen, Ngoh, Si Yan, Liew, Woei Chang, Shen, Xueyan, Hon, Lawrence S, Drake, James P, Boitano, Matthew, Hall, Richard, Chin, Chen-Shan, Lachumanan, Ramkumar, Korlach, Jonas, Trifonov, Vladimir, Kabilov, Marsel, Tupikin, Alexey, Green, Darrell, Moxon, Simon, Garvin, Tyler, Sedlazeck, Fritz J, Vurture, Gregory W, Gopalapillai, Gopikrishna, Kumar Katneni, Vinaya, Noble, Tansyn H, Scaria, Vinod, Sivasubbu, Sridhar, Jerry, Dean R, O'Brien, Stephen J, Schatz, Michael C, Dalmay, Tamás, Turner, Stephen W, Lok, Si, Christoffels, Alan, Orbán, László
Format: Article
Language:English
Subjects:
Animals
Bass - classification
Bass - genetics
Biology and Life Sciences
Chromosome Mapping
Chromosomes
Dicentrarchus labrax
DNA sequencing
Fish
Genetic aspects
Genome
Genomes
Genomics
In Situ Hybridization, Fluorescence
Inventory
Lates calcarifer
Library collections
Marine
Methods
Perciformes
Phylogeny
Population
Research and Analysis Methods
Teleostei
Zebrafish
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Summary: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.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1005954