Comparative analysis of genetic diversity and structure among four shell color strains of the Pacific oyster Crassostrea gigas based on the mitochondrial COI gene and microsatellites

Zhang, Yifei; Chen, Yulu; Xu, Chengxun; Li, Qi

doi:10.1016/j.aquaculture.2022.738990

Cited by 7 publications

(3 citation statements)

References 72 publications

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“…Microsatellites, otherwise known as simple sequence repeats (SSRs) composed of 1–6 bp tandem motifs of DNA are prominently observed throughout the eukaryotic and prokaryotic genomes (Tóth, Gáspári et al 2000, Sahu, Sahoo et al 2014, Zhang, Chen et al 2023). Their versatility is characterized by high frequency, codominance, and polymorphic in nature (Vieira, Santini et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Sahu,

Fazil,

Panda

et al. 2023

Preprint

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Microsatellite is a classical codominant marker frequently used to study genetics and evolution of living entities as well as molecular breeding in commercially important species. Although it has a tremendous application in oyster aquaculture, the lack of knowledge about its type, distribution pattern, and comparative analysis is limited. Thus, in this study, we conducted a genome-wide as well as chromosomal microsatellite landscape analysis within the genus Crassostrea. The genome-wide microsatellites number varied from 169432-212368, with relative abundance (RA) and relative density (RD) ranging from 310.18-336.5 loci/Mb and 7553.4-8793.42 bp/Mb, respectively. About 14.99-16.75% of total microsatellites were considered compound microsatellites having cRA and cRD, 21.78-25.5 loci/Mb, and 1332.81-1694.54 bp/Mb, respectively. The mononucleotide microsatellites were predominant followed by di and tetranucleotide. The RA and RD of the SSRs revealed no correlation with genome size but a significant correlation with GC content. However, the number of SSRs showed a significant relationship with the genome size but no relation with GC content. In contrast, the incidence of cSSR was positively associated with genome size and GC content. Finally, 29 cSSR loci were developed and validated inC. hongkonensisusing one wild population followed by its cross-species amplification. The allele number (Ne), observed heterozygosity (Ho), expected heterozygosity (He), inbreeding co-efficient (Fis), the polymorphic information content (PIC), ranged from 2-10, 0.092-0.897, 0.0001-1, 0.088-0.828, respectively. The present study elucidated microsatellite evolution within the Crassostrea genome and the loci developed can be utilized for brood stock analysis, parentage assignment, and construction of linkage map of the respective species.

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Section: Introductionmentioning

confidence: 99%

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Sahu,

Fazil,

Panda

et al. 2023

Preprint

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“…Compared with nuclear genes, the substitution rates of mitochondrial genes are much higher and can provide more phylogenetic information [20][21][22]. In addition, mitochondrial genes have been widely used to analyze genetic diversity [23,24] and population genetic variability in bivalves [25][26][27]. Although the animal mitochondrial gene order remains relatively conserved during long periods of evolution [6,28,29], recent studies have revealed a large number of gene rearrangement events in mitogenomes belonging to different animal Fishes 2023, 8, 528 2 of 17 groups [30][31][32].…”

Section: Introductionmentioning

confidence: 99%

Mitogenomic Analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the Evolution of the Gene Rearrangements

Zhang,

Qi,

et al. 2023

Fishes

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The complete mitogenomes of Pinctada albina and Pinctada margaritifera were sequenced in this study, with sizes of 23,841 bp and 15,556 bp, respectively. The mitochondrial genome analysis of eight Pterioidea species indicated the existence of gene rearrangements within the superfamily. The ATP8 gene was not detected in the two new mitogenomes, and rrnS was found to be duplicated in P. albina’s mitogenome. The reconstructed phylogeny based on mitogenomes strongly supported the monophyly of Pterioidea and provided robust statistical evidence of the phylogenetic relationships within Pteriomorphia. The analysis of the mitochondrial gene order revealed that of P. margaritifera to be the same as the ancestral order of Pterioidea. The gene orders of the Pterioidea species were mapped to the phylogenetic tree, and the gene rearrangement events were inferred. These results provide important insights that will support future research, such as studies extending the evolutionary patterns of the gene order from P. margaritifera to other species and determining the evolutionary status of Pterioidea within the infraclass Pteriomorphia.

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“…Investigating the genetic diversity of species is a prerequisite for the effective exploration and utilization of germplasms 8 . A high level of genetic diversity indicates strong biological survivability and environmental adaptation, which is required for sustained genetic improvement and stable inheritance of desirable traits 9 . Conversely, low genetic diversity can lead to reduced adaptability and viability, and ultimately to the degradation of species 10 .…”

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confidence: 99%

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Duan

Kang

Wan

et al. 2023

Sci Rep

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The swimming crab, Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity of P. trituberculatus in the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420 P. trituberculatus individuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI = 1.374, He = 0.687, and PIC = 0.643) in comparison with wild populations (SI ≥ 1.399, He ≥ 0.692, and PIC ≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations of P. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups of P. trituberculatus were divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.

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Comparative analysis of genetic diversity and structure among four shell color strains of the Pacific oyster Crassostrea gigas based on the mitochondrial COI gene and microsatellites

Cited by 7 publications

References 72 publications

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Mitogenomic Analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the Evolution of the Gene Rearrangements

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

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