A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans

Xu, Zhiqiang; Gao, Tianheng; Xu, Yu; Li, Xuguang; Li, Jiajia; Lin, Hai; Yan, Wei; Pan, Jianlin; Tang, Jianguo

doi:10.1016/j.ygeno.2021.07.017

Cited by 25 publications

(12 citation statements)

References 68 publications

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“…The resequencing data have been deposited in NCBI GenBank under the accession number PRJNA797570. Based on the approximately 4 Gb genome size of P. clarkii ( Shi L. et al, 2018 ; Xu et al, 2021 ), the sequencing coverage depth of each re-sequenced data point was about 30×.…”

Section: Resultsmentioning

confidence: 99%

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Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Shen

Wang

et al. 2022

Front. Genet.

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Many economic crustacean species have sex dimorphisms during their growth. Exploring the sex determination system and developing sex-specific molecular marker(s) are very helpful for carrying out sex control breeding, and next-generation sequencing has been used as an efficient way to explore them in recent years. In this study, first, the genetic sex determination system of P. clarkii was explored as an XX/XY system by analyzing the 2b-RAD sequencing data. Furthermore, DNA samples of male and female individuals from a P. clarkii family were pooled separately for whole-genome resequencing. Based on the data of whole-genome resequencing, the 9,163 male- and female-specific bias sites with higher feasibility were obtained based on the assumption of the XX/XY sex determination system, and four sites were selected to design the sex-specific marker primers. One efficient sex-specific marker was identified with a sex discrimination rate of 99.49% (195/196) when applied to five different geographical groups with 196 individuals. The results of this study would provide a foundation for the realization of P. clarkii sex control and could provide some reference for investigating the sex determination system and sex molecular marker(s) of other crustacean species based on next-generation sequencing data.

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Section: Resultsmentioning

confidence: 99%

“…The MEM (maximal exact match) module of BWA (Burrows-Wheeler aligner tool) ( Li and Durbin, 2010 ) was used to match the clean data to the reference genome of P. clarkii (PRJNA727411; Xu et al, 2021 ). The SAM files were converted to BAM files using SAMtools ( Li et al, 2009 ).…”

Section: Methodsmentioning

confidence: 99%

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Shen

Wang

et al. 2022

Front. Genet.

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“…84 Many expanded gene families are involved in the environmental tolerance of P. clarkii. 35 Similarly, the invasiveness of E. sinensis is largely attributed to its strong osmoregulatory capacity and high fertility. 83 Ecotoxicology: Many crustaceans, such as Daphnia spp., Hyalella azteca, and Tigriopus japonicus, have been used as models for ecotoxicology and evolutionary toxicology due to their sensitivity to toxicants.…”

Section: Environmental Adaptationmentioning

confidence: 99%

Recent advances in crustacean genomics and their potential application in aquaculture

Yuan

Zhang

et al. 2023

Reviews in Aquaculture

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Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans are a large group of invertebrates that encompasses some of the most important farmed species in the aquaculture industry. However, very few crustacean genomes have been published although an aquaculture genome project was proposed as early as 1997. Breakthroughs in next‐generation and third‐generation sequencing technologies and the development of high‐complexity sequence assembly strategies have promoted the publication of an increasing number of crustacean genomes, thus paving a broad way for biological and genetic studies and applications in aquaculture. In this review, we summarize recent advances in crustacean genomic research as of June 2022, including genome sequencing and assembly, genomic characteristics, and the genetic mechanisms underlying various biological phenotypes, such as environmental adaptation, lifestyle, development, and sex determination. This review also discusses the application of crustacean genomes in aquaculture, including genetic dissection of economic traits and genome‐based selective breeding via genome‐wide association studies and genomic selection. High‐quality genomes are important not only for understanding the genetic basis of biologically and economically important traits but also for the genetic improvement of aquaculture species. However, the utilization of crustacean genomics still lags far behind those in other animals. Therefore, additional multi‐omics studies and technological development are needed to accelerate the application of genomics in aquaculture.

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“… 29–31 Chromosome-level genomes have also been reported in catfishes, such as channel catfish ( Ictalurus punctatus ), 32 yellow catfish ( Pelteobagrus fulvidraco ), 33 giant devil catfish ( Bagarius yarrelli ), 34 Southern catfish ( Silurus meridionalis ), 35 Chinese longsnout catfish ( Leiocassis longirostris ), 36 striped catfish ( Pangasianodon hypophthalmus ), 37 and redtail catfish ( Hemibagrus wyckioides ). 38 These chromosome-level assemblies have been widely used as reliable reference genomes for studies of many fields, including ecological adaptation, 35 , 39 , 40 genome evolution, 41–43 gene evolution, 44 , 45 immunology, 46–48 and identification of target-trait-related genes, 49 , 50 in aquatic animals. Moreover, chromosome-level genomes have also been used for studies on sex determination mechanisms, including identification of sex determination regions and genes, 51–53 sex reversal, 54 , 55 and sex chromosome evolutions.…”

Section: Introductionmentioning

confidence: 99%

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

et al. 2022

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Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related QTLs with a PVE value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 Mb to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

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A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans

Cited by 25 publications

References 68 publications

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Recent advances in crustacean genomics and their potential application in aquaculture

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

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