Page 43 - 《水产学报》2025年第5期

瞿才惠，等 水产学报, 2025, 49(5): 059103

Distribution and comparative analysis of whole genome microsatellite in
Sebastes schlegelii and Sebastiscus marmoratus

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QU Caihui , QU Yinquan , HE Yan , ZHAO Xiang , GAO Tianxiang 1*
1. School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
2. College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
3. Fisheries College, Ocean University of China, Qingdao 266003, China

Abstract: To elucidate the distribution of microsatellites in the genomes of Sebastes schlegelii and Sebastiscus marmoratus, the
MISA software was employed to search for and compare microsatellite sequences across both genomes. The results indicated
that the total length of the S. schlegelii genome sequence was 848 024 649 bp, comprising 741 sequences, of which 635 con-
tained 534 272 microsatellite loci. The total length of microsatellite sequence was 14 151 681 bp, with an average of one
microsatellite locus per 1 587.25 bp, representing 1.67% of the genome. Of the sequences containing microsatellite loci, 584
(91.97%) contained more than one locus, while 51 (8.03%) contained a single locus. The ratios of different repeat types of
microsatellites, ranked by size, were as follows: di-nucleotide (46.37%) > mono-nucleotide (30.97%) > tri-nucleotide (15.42%)
> tetra-nucleotide (5.7%) > penta-nucleotide (1.19%) > hexa-nucleotide (0.35%). For S. marmoratus, the total genome
sequence length was 795 691 141 bp, with a total of 90 sequences. Among these, 77 sequences contained 571 370 microsatel-
lite loci. The total length of microsatellite sequences was 15 854 826 bp, with an average of one microsatellite locus per 1
392.60 bp, accounting for 1.99% of the genome. Of the sequences containing microsatellite locus, 74 (96.10%) contained more
than one locus, while 3 (3.70%) sequences contained a single locus. The ratios of different repeat types of microsatellites,
ranked by size, were di-nucleotide (47.63%) > mono-nucleotide (32.90%) > tri-nucleotide (13.63%) > tetra-nucleotide (4.26%)
> penta-nucleotide (1.04%) > hexa-nucleotide (0.53%). Our findings demonstrate that the microsatellites of different repeat
types in S. schlegelii and S. marmoratus exhibit similar characteristics. Additionally, as the amplification length of microsatel-
lite sequences increased, the frequency of nucleotides in both fish species showed a gradual downward trend. This study,
which compared the distribution of microsatellites in the genomes of S. schlegelii and S. marmoratus, provided a foundation for
future research on microsatellite marker screening, genetic analysis, and molecular breeding of these two species.
Key words: Sebastes schlegelii; Sebastiscus marmoratus; whole genome; microsatellite; characteristics analysis
Corresponding author: GAO Tianxiang. E-mail: gaotianxiang0611@163.com
Funding projects: National Natural Science Foundation of China (32072966)

https://www.china-fishery.cn 中国水产学会主办 sponsored by China Society of Fisheries
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