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Genome survey of Misgurnus anguillicaudatus to identify genomic information, simple sequence repeat (SSR) markers, and mitochondrial genome

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Abstract

Background

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.

Methods and results

In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb 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).

Conclusions

This is the first report of genome survey sequencing in M. anguillicaudatus, 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.

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Data availability

The data used to support the findings of this study are available from the article and its supplementary information.

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Acknowledgements

This study was supported by China Agriculture Research System of MOF and MARA (CARS-46) and the National Key R&D Program of China (No. 2018YFD0901201).

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Authors and Affiliations

  1. College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, China

    Guiyun Huang & Gang Chen

  2. Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China

    Guiyun Huang, Jianmeng Cao, Miao Wang, Zhigang Liu, Fengying Gao, Mengmeng Yi & Maixin Lu

  3. Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Aquatic Germplasm Resources and Genetic Breeding Library, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China

    Chen Chen

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Contributions

Conceived and designed the experiments: GC ML. Performed the experiments, analyzed the genetic data: GH. Contributed reagents/materials/analysis tools: JC CC MW ZL FG MY. Wrote the paper: GH ML. All authors read, revised, and approved the manuscript.

Corresponding authors

Correspondence to Gang Chen or Maixin Lu.

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Conflict of interest

The authors declare no conflict of interest.

Ethical approval

All experimental procedures for loach handling were approved by the Animal Care and Ethics Committee of the Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences.

Consent to participate

This study was conducted at Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences. The institution and all authors agreed to participate in this research.

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The Author confirms: that the work described has not been published before; that it is not under consideration for publication elsewhere; that its publication has been approved by all co-authors if any; that its publication has been approved explicitly by the responsible authorities at the institution where the work is carried out. The authors agree to publication in the journal Molecular Biology Reports.

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Huang, G., Cao, J., Chen, C. et al. Genome survey of Misgurnus anguillicaudatus to identify genomic information, simple sequence repeat (SSR) markers, and mitochondrial genome. Mol Biol Rep 49, 2185–2196 (2022). https://doi.org/10.1007/s11033-021-07037-x

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