Wu Baocheng, Wen Jun, Lu Ruisen, Zhou Wei
Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, Jiangsu, China.
Front Genet. 2024 Aug 14;15:1368760. doi: 10.3389/fgene.2024.1368760. eCollection 2024.
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 Hassk., which is native to East Asia. Our study aimed to assess the species status of according to its genetic structure and genetic diversity patterns among 66 naturally distributed populations, comprising 26 f. , 36 f. (Y. Yabe) Hara and 4 f. 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 , and 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 analysis showed significant ( < 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 , and values highlighted the middle latitude area of East Asia as a significant contributor to genetic structuring in . Overall, our study elucidates the relatively low genetic differentiation and population structure of across East Asia, further enhancing our understanding of plant lineage diversification in the Sino-Japanese Floristic Region.
单核苷酸多态性（SNPs）是基因组多态性最普遍的形式，广泛应用于群体遗传学研究。我们使用一种高通量测序方法——dd-RAD测序，研究了广泛分布于东亚的分类群Hassk.的三种形态类型之间的基因组水平多样性、种群结构和系统发育关系。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，评估Hassk.的物种地位，这些种群包括26个原变种、36个变种（矢部义方）原和4个变型刘慎愕的材料。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、邻接法（NJ）系统发育、混合聚类和种群分化分析。研究结果如下：（1）共产生了539946个无连锁的高质量SNP，其平均MAF、Het、DP和Fst值分别为0.062、0.066、0.043和-0.014；（2）种群分化不受距离隔离的影响；（3）确定了六个与地理位置相对应且表现出不同遗传多样性水平的主要不同区域；（4）成对Fst分析表明，在进行连续Bonferroni校正后，六个区域中0%-至14%的种群存在显著（P<0.05）的种群分化；（5）三个迁移事件（历史基因流）表明了东西方向。此外，使用Jost's D、Nei's Gst和Nm值进行的当代基因流分析突出了东亚中纬度地区是Hassk.遗传结构的重要贡献者。总体而言，我们的研究阐明了Hassk.在东亚地区相对较低的遗传分化和种群结构，进一步加深了我们对中日植物区系中植物谱系多样化的理解。
