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

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A., Orban, L. (April 2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12 (4). e1005954. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/27082250
DOI: 10.1371/journal.pgen.1005954

Abstract

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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
Investigative techniques and equipment > assays > next generation sequencing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
Watson School > Publications
Depositing User: Matt Covey
Date: 15 April 2016
Date Deposited: 13 May 2016 19:19
Last Modified: 03 Jan 2019 19:19
PMCID: PMC4833346
Related URLs:
URI: http://repository.cshl.edu/id/eprint/32795

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