Isolation and characterization of eleven microsatellite loci in the marbled rockfish, Sebastiscus marmoratus (Scorpaenidae)

Li, Qinghui; Li, Zhongbao; G, Dai; Cao, Yuanyu; Chen, Xiao-Jiao; Chen, Lina; Shangguan, Jingbo; Ning, Yue

doi:10.1007/s12686-013-0001-y

Cited by 9 publications

(5 citation statements)

References 3 publications

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“…The dinucleotide repeats were dominant (53.70%), followed by trinucleotide repeats (35.36%), hexanucleotide repeats (4.59%), tetranucleotide repeats (4.57%) and pentanucleotide repeats (1.77%). According to the distribution and frequency of microsatellite motifs, the dinucleotide repeats had the highest number and type of repeats, which was similar to the previous studies of other fish, such as Pseudosciaena crocea [37] and Megalobrama amblycephala [38]. The frequency of repetitions decreases exponentially with the length of the repetitions, because long mutations have high mutation rates [39].…”

Section: Identification Of Ssrsupporting

confidence: 84%

Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

et al. 2020

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Acanthogobius ommaturus is one of the suitable species to study the genetic mechanism of adaptive evolution, but there are few reports on its genetics. In this study, the genomic survey sequencing method was used to analyze the genome characters of A. ommaturus. A total of 50.50 G high-quality sequence data was obtained in the present study. From the 19-mer distribution frequency, the estimated genome size was 928.01 Mb. The calculated sequence repeat rate was about 38.31%, the heterozygosity was about 0.17%, and the GC% content was about 40.88%. Moreover, 475,724 simple sequence repeats (SSRs) were identified. Among them, dinucleotide repeats were the most (53.70% of the total SSRs), followed by tri- (35.36%), hexa- (4.59%), tetra- (4.57%) and penta- (1.77%) nucleotide repeats type. This is the first genome-wide feature of this species to be reported.

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Section: Identification Of Ssrsupporting

confidence: 84%

Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

et al. 2020

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“…Among them, di-nucleotide repeats were the most abundant (1,970,270, 87.00%) followed by tri-nucleotide repeats (236,541, 10.45%), tetra-nucleotide repeats (43,907, 1.94%), penta-nucleotide repeats (977,333, 0.34%), and hexa-nucleotide repeats (6196, 0.27%). The tendency of di-nucleotide repeats frequency in the studied species was similar to that in other fish species, such as Pseudosciaena crocea and Megalobrama amblycephala [ 26 , 27 ]. Furthermore, this result was consistent with data indicating that the repeat frequency decreases with the increase in repeat length because long mutations are related to high mutation rates [ 28 ].…”

Section: Resultssupporting

confidence: 75%

A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913

Choi

Kim

Lee

et al. 2021

Animals

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Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

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“…Using assembled draft genome data of C. dewitti , 2 252 265 microsatellite motifs were identified, of which dinucleotide repeats (1,920,127; 85.25%) occupied the largest proportion of all repeat motifs. The frequency of di-nucleotide repeats in C. dewitti species was comparable to that of other fish species evaluated, such as Pseudosciaena crocea and Megalobrama amblycephala [ 31 , 32 ]. Furthermore, because long mutations are associated with high mutation rates, this result was consistent with data demonstrating that repeat frequency declines with increasing repeat length [ 22 ].…”

Section: Resultssupporting

confidence: 62%

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti

Kim

Lee

et al. 2022

Animals

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The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers.

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Isolation and characterization of eleven microsatellite loci in the marbled rockfish, Sebastiscus marmoratus (Scorpaenidae)

Cited by 9 publications

References 3 publications

Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti

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