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Article

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

by
Kang-Rae Kim
1,†,
So Young Park
1,†,
Ju Hui Jeong
1,
Yujin Hwang
1,
Heesoo Kim
1,
Mu-Sung Sung
2 and
Jeong-Nam Yu
1,*
1
Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
2
Muldeuli Research, Icheon 12607, Republic of Korea
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(12), 6689; https://doi.org/10.3390/ijms25126689
Submission received: 20 May 2024 / Revised: 13 June 2024 / Accepted: 14 June 2024 / Published: 18 June 2024
(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Molecular Research)
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Abstract

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.
Keywords: genome assembly; Rhodeus uyekii; population genetics; bottleneck; microsatellite genome assembly; Rhodeus uyekii; population genetics; bottleneck; microsatellite

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MDPI and ACS Style

Kim, K.-R.; Park, S.Y.; Jeong, J.H.; Hwang, Y.; Kim, H.; Sung, M.-S.; Yu, J.-N. Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly. Int. J. Mol. Sci. 2024, 25, 6689. https://doi.org/10.3390/ijms25126689

AMA Style

Kim K-R, Park SY, Jeong JH, Hwang Y, Kim H, Sung M-S, Yu J-N. Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly. International Journal of Molecular Sciences. 2024; 25(12):6689. https://doi.org/10.3390/ijms25126689

Chicago/Turabian Style

Kim, Kang-Rae, So Young Park, Ju Hui Jeong, Yujin Hwang, Heesoo Kim, Mu-Sung Sung, and Jeong-Nam Yu. 2024. "Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly" International Journal of Molecular Sciences 25, no. 12: 6689. https://doi.org/10.3390/ijms25126689

APA Style

Kim, K.-R., Park, S. Y., Jeong, J. H., Hwang, Y., Kim, H., Sung, M.-S., & Yu, J.-N. (2024). Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly. International Journal of Molecular Sciences, 25(12), 6689. https://doi.org/10.3390/ijms25126689

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