单核苷酸多态性(SNP)代表了基因组多态性的最普遍形式,并被广泛用于群体遗传学研究。使用dd-RAD测序,一种高通量测序方法,我们调查了基因组水平的多样性,人口结构,以及广泛分布的日本隐虫Hassk分类单元的三种形态之间的系统发育关系。,原产于东亚。我们的研究旨在根据66个自然分布种群的遗传结构和遗传多样性模式来评估C.japonica的物种状况。包括26个粳稻,36C.japonicaf.dissecta(Y.Yabe)Haraand4C.japonicaf.pinnatisectaS.L.基于dd-RAD测序产生的基因组SNP数据,我们进行了遗传多样性,主成分,邻居连接(NJ)系统发育,外加剂聚类,和人口分化分析。调查结果揭示了以下内容:(1)5,39,946个未链接,高质量的SNP,平均π,HO,HE和FIS值分别为0.062、0.066、0.043和-0.014,产生;(2)种群差异不受远距离隔离的影响;(3)确定了与地理位置相对应并表现出不同水平的遗传多样性的六个主要不同区域;(4)成对FST分析显示,经过连续Bonferroni校正后,六个地区中有0%-14%的种群存在显着差异(P<0.05);(5)三个迁移事件(历史基因流)表明东向西方向。此外,使用Jost\'sD进行当代基因流分析,Nei\'sGST,和Nm值强调了东亚中纬度地区是粳稻遗传结构的重要贡献者。总的来说,我们的研究阐明了整个东亚地区的日本花青素相对较低的遗传分化和种群结构,进一步加深我们对中日植物区系多样化的认识。
Single-nucleotide polymorphisms (SNPs) represent the most prevalent form of genomic polymorphism and are extensively used in population genetics research. Using dd-RAD sequencing, a high-throughput sequencing method, we investigated the genome-level diversity, population structure, and phylogenetic relationships among three morphological forms of the widely distributed taxon Cryptotaenia japonica Hassk., which is native to East Asia. Our study aimed to assess the species status of C. japonica according to its genetic structure and genetic diversity patterns among 66 naturally distributed populations, comprising 26 C. japonica f. japonica, 36 C. japonica f. dissecta (Y. Yabe) Hara and 4 C. japonica f. pinnatisecta S. L. Liou accessions. Based on genomic SNP data generated by dd-RAD sequencing, we conducted genetic diversity, principal component, neighbor-joining (NJ) phylogenetic, admixture clustering, and population differentiation analyses. The findings revealed the following: (1) 5,39,946 unlinked, high-quality SNPs, with mean π, H O, H E and F IS values of 0.062, 0.066, 0.043 and -0.014, respectively, were generated; (2) population divergence was unaffected by isolation through distance; (3) six main distinct regions corresponding to geographic locations and exhibiting various levels of genetic diversity were identified; (4) pairwise F ST analysis showed significant (P < 0.05) population differentiation in 0%-14% of populations among the six regions after sequential Bonferroni correction; and (5) three migration events (historical gene flow) indicated east‒west directionality. Moreover, contemporary gene flow analysis using Jost\'s D, Nei\'s G ST, and Nm values highlighted the middle latitude area of East Asia as a significant contributor to genetic structuring in C. japonica. Overall, our study elucidates the relatively low genetic differentiation and population structure of C. japonica across East Asia, further enhancing our understanding of plant lineage diversification in the Sino-Japanese Floristic Region.