1. A chromosome-level assembly of the black tiger shrimp ( Penaeus monodon ) genome facilitates the identification of novel growth-associated genes
- Author
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Wirulda Pootakham, Kanchana Sittikankaew, Frédéric Tangy, Piroon Jenjaroenpun, Jasper J. Koehorst, Intawat Nookaew, Tanaporn Uengwetwanit, Wanilada Rungrassamee, Peter J. Schaap, Pacharaporn Angthong, Jutatip Khudet, Sopacha Arayamethakorn, Rungnapa Leelatanawit, Duangjai Sangsrakru, Vitor A. P. Martins dos Santos, Thidathip Wongsurawat, Chutima Sonthirod, Nitsara Karoonuthaisiri, National Center for Genetic Engineering and Biotechnology [Thailand] (BIOTEC), National Science and Technology Development Agency [Bangkok] (NSTDA), University of Arkansas for Medical Sciences (UAMS), Shrimp Genetic Improvement Center [Thani, Thailand] (SGIC), National Science and Technology Development Agency [Bangkok] (NSTDA)-National Science and Technology Development Agency [Bangkok] (NSTDA), Department of Agrotechnology and Food Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Génomique virale et vaccination, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This project was funded by National Center for Genetic Engineering and Biotechnology (BIOTEC Platform No. P1651718), TDG Food and Feed program, National Science and Technology Development Agency (No. P1950419) and partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734486 (SAFE-Aqua)., Visiting Professor Program 2019 was awarded to Dr. Intawat Nookaew by the National Science and Technology Development Agency, Thailand., The authors acknowledge NSTDA Supercomputer Center (ThaiSC) for providing HPC resources that have contributed to the research results reported within this paper. We thank Ms. Somjai Wongtripop, Mr. Kaidtisak kaewlok and Shrimp Genetic Improvement Center (SGIC) members, as well as Ms. Sudtida Phuengwas (BIOTEC) for the shrimp sample collection., We acknowledge Zulema Dominguez (University of Arkansas for Medical Sciences, USA) for technical assistance on comparative genome. We are grateful to Prof. Morakot Tanticharoen (NSTDA), Dr. Kanyawim Kirtikara (BIOTEC), Dr. Wonnop Visessanguan (BIOTEC) and Assoc Prof. Skorn Koonawootrittriron (Kasetsart University, Thailand) for their mentorship on the shrimp research programs., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
growth-associated ,[SDV]Life Sciences [q-bio] ,Sequence assembly ,Computational biology ,Genome ,Penaeus monodon ,03 medical and health sciences ,transcriptomics ,Hi-C ,14. Life underwater ,Black tiger shrimp ,genes ,Genome size ,reference genome ,030304 developmental biology ,2. Zero hunger ,Comparative genomics ,Whole genome sequencing ,PacBio ,0303 health sciences ,biology ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,04 agricultural and veterinary sciences ,Genome project ,biology.organism_classification ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Reference genome - Abstract
The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available 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 in this species. 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%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel 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 gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.
- Published
- 2020