Abstract
The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data for M. anguillicaudatus is currently unavailable. In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified, and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides,the complete mitochondrial genome was sequenced. Based on the Maximum Likelihood and Bayesian inference analyses, M. anguillicaudatus yingde in this study was the "introgressed" mitochondrial type. Seventy microsatellite loci were randomly selected from detected SSR loci to test polymorphic, of which, 20 microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All 20 loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.05). This is the first report of genome survey sequencing in M. anguillicaudatus, genome information, mitochondrial genome, andmicrosatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.
Highlights
Next-generation, high-throughput sequencing (NGS) is a cost-efficient strategy for generating genomic resources
Eight loci deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). This is the first report of a genome survey in M. anguillicaudatus, and genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding
Based on genome survey sequencing, many high-quality SSR markers have been developed in aquaculture species such as Charybdis feriatus [9], Sillago sihama [10], Marsupenaeus japonicus [2], and Hemibagrus wyckioides [11]
Summary
Next-generation, high-throughput sequencing (NGS) is a cost-efficient strategy for generating genomic resources. Genome survey sequencing via NGS provides information on the genome structure of a species, such as the genome size, heterozygosity, and repeat contents. Genome survey sequencing has been widely used to accurately predict the whole genome characteristics of aquaculture species and played an important role in evolutionary biology and adaptation survey [1,2,3,4,5]. In addition to genome information, genome survey sequencing can generate a large amount of sequence data for the development of molecular markers, such as microsatellites and SNP. Based on genome survey sequencing, many high-quality SSR markers have been developed in aquaculture species such as Charybdis feriatus [9], Sillago sihama [10], Marsupenaeus japonicus [2], and Hemibagrus wyckioides [11]
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