Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae)

Yin, Lina; Zhang, Hui; Yanagimoto, Takashi; Gao, Tianxiang

doi:10.1134/s1022795412120174

Cited by 5 publications

(2 citation statements)

References 7 publications

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“…However, inconsistent results were demonstrated given the insufficient resolution of molecular markers. Till now, limited microsatellite marker resources are publically available for S. marmoratus using different methods [18][19][20][21][22]. The use of microsatellite markers in molecular studies is limited and more microsatellite markers are needed for further studies.…”

Section: Introductionmentioning

confidence: 99%

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Song

Xiao

et al. 2020

Bioscience Reports

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The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

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Section: Introductionmentioning

confidence: 99%

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Song

Xiao

et al. 2020

Bioscience Reports

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“…However, most of these studies in S. marmoratus were related to physiological and ecological aspects of the species (Mizue, 1959;Shiokawa, 1962;Watanabe, 2003;Yoko et al, 2006;Wang et al, 2005Wang et al, , 2009. Few microsatellite markers have been developed to examine genetic variation (Xu et al, 2010;Yin et al, 2012;Li et al, 2013). The number of appropriate polymorphic markers is insufficient to carry out phylogenetic and population genetic on this species.…”

Section: Introductionmentioning

confidence: 99%

Isolation of new polymorphic microsatellite markers from the marbled rockfish Sebastiscus marmoratus

Deng¹,

Li²,

G³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The marbled rockfish, Sebastiscus marmoratus, is an important commercially near-shore fish that inhabits the beach rocky bottom from Japan to the South China Sea. Eleven polymorphic microsatellite loci were developed from S. marmoratus and were used to identify polymorphisms in 30 samples from a wild population. The allele locus number ranged from 2 to 7. Polymorphism data content ranged from 0.032 to 0.751. The observed and expected heterozygosity levels were 0.0333-0.9667 and 0.0328-0.7675, respectively. Two loci, Smd1-112 and Smd2-80, deviated from Hardy-Weinberg equilibrium. These polymorphic microsatellite markers will facilitate further studies of genetic diversity and genetic differentiation of S. marmoratus.

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Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

Song

Chen

Gao

et al. 2016

Chin. J. Ocean. Limnol.

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Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae)

Cited by 5 publications

References 7 publications

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Isolation of new polymorphic microsatellite markers from the marbled rockfish Sebastiscus marmoratus

Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

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