Genomic characteristics and profile of microsatellite primers for <i>Acanthogobius ommaturus</i> by genome survey sequencing

Chen, Bingjie; Sun, Zhicheng; Lou, Fangrui; Gao, Tianxiang; Song, Na

doi:10.1042/bsr20201295

Cited by 18 publications

(13 citation statements)

References 33 publications

(43 reference statements)

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“…Among them, dinucleotide motifs were the most prevalent (1926231; 86.87%), followed by trinucleotides (249028; 11.23%), tetranucleotides (36955; 1.67%), pentanucleotides (3372; 0.15%), and hexanucleotides (1836; 0.08%) ( Table 4 and Figure 2 A). The tendency of the motif frequency in the studied species was similar to that in other fish species, with the dinucleotide motif being predominant [ 33 , 34 ]. In the dinucleotides, the most frequent motif was AC/GT (71.84%), followed by AG/CT (17.29%), AT/AT (10.82%), and CG/CG (0.05%) ( Figure 2 B).…”

Section: Resultssupporting

confidence: 71%

Genome survey and microsatellite motif identification ofPogonophryne albipinna

Cho

Lee

et al. 2021

Bioscience Reports

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The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ~883.8 Mb by K-mer analysis (K=25), and the heterozygosity and repeat ratio were 0.289% and 39.03%, respectively. The genome sequences were assembled into 571,624 contigs, covering a total length of ~819.3 Mb with an N50 of 2,867 bp. A total of 2,217,422 simple sequence repeat motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole genome sequencing of P. albipinna.

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Section: Resultssupporting

confidence: 71%

Genome survey and microsatellite motif identification ofPogonophryne albipinna

Cho

Lee

et al. 2021

Bioscience Reports

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“…As both sister chromatids would be separately assembled in high-heterozygosity regions, it might cause the imprecise assessment of genome size. The heterozygosity ratio of H. nehereus observed in the present study was 0.67%, which was higher than that of Scatophagus argus (female 0.37% and male 0.38%) [47], Sebastiscus marmoratus (0.17%) [48] and Acanthogobius ommaturus (0.17%) [49], but smaller than that of Sillago sihama (0.92%) [50]. Genome assembly becomes more difficult when the heterozygosity ratio is higher than 0.5% [25].…”

Section: Discussioncontrasting

confidence: 65%

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Yang

Huang

Ning

et al. 2021

CIMB

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Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.

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“…Microsatellite DNA marker offers several advantages of codominant, extensive distribution, abundant polymorphisms and convenient analysis, and has become an ideal tool in genetics and evolution studies [ 45 ]. In the present study, the dinucleotide repeats had the highest number and type of repeats, which was consistent with Acanthogobius ommaturus [ 46 ], Sillago sihama [ 47 ], Harpadon nehereus [ 48 ] and Cociella crocodilus [ 49 ]. SSR polymorphic loci are mainly distributed in dinucleotide and trinucleotide repeats [ 50 ].…”

Section: Discussionsupporting

confidence: 87%

Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform

et al. 2022

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Ophichthidae fishes limit to continental shelf of all tropical and subtropical oceans, and contain more than 350 species, representing the greatest specialization diversity in the order Anguiliformes. In this study, we conducted a genome survey sequencing (GSS) analysis of Ophichthus evermanni by Illumina sequencing platform to briefly reveal its genomic characteristics and phylogenetic relationship. The first de novo assembled 1.97 Gb draft genome of O. evermanni was predicted based on K-mer analysis without obvious nucleotide bias. The heterozygosity ratio was 0.70%, and the sequence repeat ratio was calculated to be 43.30%. A total of 9,016 putative coding genes were successfully predicted, in which 3,587 unigenes were identified by gene ontology (GO) analysis and 4,375 unigenes were classified into cluster of orthologous groups for enkaryotic complete genomes (KOG) functional categories. About 2,812,813 microsatellite motifs including mono-, di-, tri-, tetra-, penta-, and hexanucleotide motifs were identified, with an occurrence frequency of 23.32%. The most abundant type was dinucleotide repeat motifs, accounting for 49.19% of the total repeat types. The mitochondrial genome, as a byproduct of GSS, was assembled to investigate the evolutionary relationships between O. evermanni and its relatives. Bayesian inference (BI) phylogenetic tree inferring from concatenated 12 protein-coding genes (PCGs) showed complicated relationships among Ophichthidae species, indicating a polyphyletic origin of the family. The results would achieve more thorough genetic information of snake eels and provide a theoretical basis and reference for further genome-wide analysis of O. evermanni.

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

Cited by 18 publications

References 33 publications

Genome survey and microsatellite motif identification ofPogonophryne albipinna

Genome survey and microsatellite motif identification ofPogonophryne albipinna

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform

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