A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes

Tanaporg 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, J.J. Koehorst, P.J. Schaap, V.A.P. Martins dos Santos, Frédéric Tangy, Nitsara Karoonuthaisiri*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

43 Citations (Scopus)


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.
Original languageEnglish
Pages (from-to)1620-1640
JournalMolecular Ecology Resources
Issue number5
Early online date15 Feb 2021
Publication statusPublished - 2021


  • black tiger shrimp
  • growth-associated genes
  • Hi-C
  • PacBio
  • Penaeus monodon
  • reference genome
  • transcriptomics


Dive into the research topics of 'A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes'. Together they form a unique fingerprint.

Cite this