Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Abstract

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.

Whole genome survey and microsatellite motif identification ofArtemia franciscana

“…The types of motifs contained 77.22% (325,450) dinucleotide, 20.38% (85,912) trinucleotide, 2.11% (8,877) tetranucleotide, 0.20% (838) pentanucleotide, and 0.09% (390) hexanucleotide ( Table 3). The percentage of dinucleotide repeats was the highest, and as the repeat motif length increased, the number of loci decreased, similar to other studies (13,24,25). It has been suggested that longer repeats have higher mutation rates, causing instability (26,27) and shorter persistence times because of their downward mutation bias toward a reduction in repeat number (28).…”

“…Genome survey sequencing (GSS) using next-generation sequencing (NGS) is a time-and costeffective way to evaluate genome information, such as genome size, heterozygosity level, and repeat content, and can be used to develop molecular markers (13,14). Simple sequence repeats (SSRs) or microsatellites are short tandem repeats of 1-6 nucleotides that have been utilized as genetic markers because of their outstanding abundance and high variability (15).…”

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

“…The clean reads were assembled into contigs in software SOAPdenovo (v2.01, https://github.com/aquaskyline/SOAPdenovo2/ ) by applying the de Bruijn graph structure [ 26 ]. The paired-end information was then used to join the unique contigs into scaffolds [ 11 ]. To assess the completeness of the assembly, a Benchmarking Universal Single-Copy Orthologs (BUSCO, v.4.0, https://busco.ezlab.org/ ) evaluation was performed using the Eukaryota vertebrata_odb10 database [ 27 ].…”

“…At present, high-throughput next-generation sequencing (NGS) is the main method of genome investigation, which is an important and effective strategy to generate genetic and genomic information [11]. Genome survey sequencing bases on the low-depth sequencing data of the small fragment library [12], and can effectively evaluate the genome size, GC content and heterozygosity through K-mer analysis [13,14].…”

“…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.…”