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

Uengwetwanit, Tanaporn; Pootakham, Wirulda; Nookaew, Intawat; Sonthirod, Chutima; Angthong, Pacharaporn; Sittikankaew, Kanchana; Rungrassamee, Wanilada; Arayamethakorn, Sopacha; Wongsurawat, Thidathip; Jenjaroenpun, Piroon; Sangsrakru, Duangjai; Leelatanawit, Rungnapa; Khudet, Jutatip; Koehorst, Jasper J.; Schaap, Peter J.; Santos, Vítor Martins dos; Tangy, Frédéric; Karoonuthaisiri, Nitsara

doi:10.1111/1755-0998.13357

Cited by 63 publications

(68 citation statements)

References 147 publications

(158 reference statements)

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“…For polyploidy genome, the peaks at 25, 50, and 75% would be expected. (Zhang et al, 2019;Uengwetwanit et al, 2021;Yuan et al, 2021). LINE, long interspersed nuclear element; LTR, long terminal repeat; SINE, short interspersed nuclear element.…”

Section: Repeats In the Penaeid Shrimp Genomesmentioning

confidence: 99%

“…However, the detailed mechanisms of these biological features are far from understood. Thus, numerous recent studies have tried to investigate these mechanisms through whole-genome sequencing (WGS) of penaeid shrimp ( Yuan et al, 2018 , 2021 ; Zhang et al, 2019 ; Uengwetwanit et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…However, due to the high degree of genome complexity, penaeid shrimp has encountered extreme difficulties in genome sequencing and assembly, and the first penaeid shrimp genome was not completed until 2019 ( Zhang et al, 2019 ). Nowadays, only three high-quality genomes of penaeid shrimp have been reported, namely, L. vannamei , F. chinensis , and P. monodon ( Zhang et al, 2019 ; Uengwetwanit et al, 2021 ; Yuan et al, 2021 ). The draft assembly of M. japonicus is highly fragmented ( Yuan et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

Yuan

Zhang

et al. 2021

Front. Genet.

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Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.

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Section: Repeats In the Penaeid Shrimp Genomesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

Yuan

Zhang

et al. 2021

Front. Genet.

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“…Zhang et al, 2019). The lower repetitive sequences proportion could contribute to the genome contraction, but not be the dominant factor, because the P. monodon , which closer to F. chinensis in evolution, has a similar repetitive sequences proportion with F. chinensis (62.5%), but the genome size is also bigger (2.59 Gb) (Uengwetwanit et al, 2021).…”

Section: The Genome Of F Chinensis Contracted Compared To Other Penaeid Shrimpsmentioning

confidence: 99%

“…Zhang et al, 2019), covering 1.66 Gb in 4,683 scaffolds, with N50 length of 605.56 Kb, and was improved to 31.30 Mb by using Hi-C technology (Yuan et al, 2021). Two genomic resources for another Penaeus species, Penaeus monodon , was released lately (Uengwetwanit et al, 2021;Van Quyen et al, 2020); the improved genome was generated using long-read PacBio and long-range Chicago, producing a final genome assembly of 2.39 Gb, with contig N50 length of 79 Kb (Uengwetwanit et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

High-quality genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests genome contraction and adaptation to the environment

Wang¹,

Ren²,

Liu³

et al. 2021

Preprint

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A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1,465.32 Mb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.

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Epigenetics in Crustaceans

Vogt

2023

Epigenetics in Aquaculture

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

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 63 publications

References 147 publications

Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

High-quality genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests genome contraction and adaptation to the environment

Epigenetics in Crustaceans

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