Publication: A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes
Issued Date
2021-07-01
Resource Type
ISSN
17550998
1755098X
1755098X
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2-s2.0-85102497883
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Mahidol University
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SCOPUS
Bibliographic Citation
Molecular Ecology Resources. Vol.21, No.5 (2021), 1620-1640
Suggested Citation
Tanaporn Uengwetwanit, Wirulda Pootakham, Intawat Nookaew, Chutima Sonthirod, Pacharaporn Angthong, Kanchana Sittikankaew, Wanilada Rungrassamee, Sopacha Arayamethakorn, Thidathip Wongsurawat, Piroon Jenjaroenpun, Duangjai Sangsrakru, Rungnapa Leelatanawit, Jutatip Khudet, Jasper J. Koehorst, Peter J. Schaap, Vitor Martins dos Santos, Frédéric Tangy, Nitsara Karoonuthaisiri A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. Molecular Ecology Resources. Vol.21, No.5 (2021), 1620-1640. doi:10.1111/1755-0998.13357 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/75639
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Title
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes
Author(s)
Tanaporn Uengwetwanit
Wirulda Pootakham
Intawat Nookaew
Chutima Sonthirod
Pacharaporn Angthong
Kanchana Sittikankaew
Wanilada Rungrassamee
Sopacha Arayamethakorn
Thidathip Wongsurawat
Piroon Jenjaroenpun
Duangjai Sangsrakru
Rungnapa Leelatanawit
Jutatip Khudet
Jasper J. Koehorst
Peter J. Schaap
Vitor Martins dos Santos
Frédéric Tangy
Nitsara Karoonuthaisiri
Wirulda Pootakham
Intawat Nookaew
Chutima Sonthirod
Pacharaporn Angthong
Kanchana Sittikankaew
Wanilada Rungrassamee
Sopacha Arayamethakorn
Thidathip Wongsurawat
Piroon Jenjaroenpun
Duangjai Sangsrakru
Rungnapa Leelatanawit
Jutatip Khudet
Jasper J. Koehorst
Peter J. Schaap
Vitor Martins dos Santos
Frédéric Tangy
Nitsara Karoonuthaisiri
Other Contributor(s)
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.