A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta , using Ion Torrent technology

Adelyna, M. A. Noor; Jung, Hyungtaek; Chand, Vincent; Mather, Peter B.; Azizah, Mohd Nor Siti

doi:10.1016/j.mgene.2016.10.005

Cited by 7 publications

(4 citation statements)

References 33 publications

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“…Genome survey sequencing (GSS) based on the NGS platform has been proven particularly useful in identifying genome-wide microsatellite markers in non-model species. Microsatellite markers development studies from GSS were performed in numbers of species [9][10][11][12][13]. Genome survey studies also provide information about genome structure of organisms, including estimates of genome size, levels of heterozygosity, and repeat contents.…”

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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“…Therefore, in the present study, based on high-throughput sequencing, K -mer analysis was used to investigate the genomic characteristics of A. ommaturus and also give profile of its microsatellite primers. The results of the present study will provide theoretical basis for the subsequent development of the whole genome de novo sequencing assembly strategy [ 11 , 19 ], and can be used to describe the genetic background of many other marine animals [ 11 , 20–22 ]. In addition, the draft genome that is obtained by this sequencing is also conducive to the detecting of SNP loci.…”

Section: Introductionmentioning

confidence: 99%

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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“…The heterozygosity index of R. brachysoma (0.813) is slightly higher than that of R. kanagurta (0.808). Some years ago, Adelyna et al [ 25 ] performed a genome survey and identified microsatellite markers in R. brachysoma using the Ion Torrent sequencing platform. The results provided only a partial genome survey since the low-depth sequencing coverage of 81.28 Mbp enabled them to assemble only short contigs.…”

Section: Resultsmentioning

confidence: 99%

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta)

Surachat

Narkthewan

Thotsagotphairee

et al. 2022

Animals

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Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.

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A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta , using Ion Torrent technology

Cited by 7 publications

References 33 publications

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

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

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta)

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