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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.
摘要：
这项研究是表征Rhodusuyekii基因组并研究微卫星标记及其应用于野生种群遗传结构的开发的第一份报告。基因组组装基于PacBioHiFi和IlluminaHiSeq配对末端测序，导致了R.uyekii的基因组组装草案。将草图基因组组装成2652个重叠群。组件的完整性评估表明草案组件的质量很高，Verbrata数据库中有3259个完整的BUSCOs(97.2%)。在蛋白质数据库中注释了总共31,166个预测的蛋白质编码基因。系统发育树显示，杜氏毛虫是巨毛甲虫的近亲但不同的亲戚。在10个鱼类基因组中，有显著的基因家族扩增(8-2387)和收缩(16-2886)。通过21个多态性标记扩增的等位基因的平均数量为6至23个，平均PIC值为0.753，这将对进化和遗传分析有用。利用群体遗传分析，我们分析了来自6个种群的120个个体的遗传多样性和遗传结构。每个群体的平均等位基因数在7.6到9.9之间，观察到的杂合性在0.496到0.642之间，预期杂合性在0.587到0.783之间。主成分的判别分析根据分析方法，人口分为三个群体(BS与DCvs.GG,GC,MS,DC)。总之,我们的研究为比较基因组学提供了有用的资源，系统发育,和未来的人口研究。
