Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
Nineteen samples of Gardenia jasminoides Ellis from China were used for genome resequencing. The clean Q30 base rates ranged from 91.19% to 92.94%. When mapping with the reference genome, a total of 7,568,199 inDel sites and 61,535,595 SNP sites were detected, with variations of heterozygosity ratios ranging from 44.86% to 92.69% and from 41.53% to 90.38%, respectively. Genome location and function annotation of SNP and inDel in different samples were carried out. SNP and inDel were mainly located in the intergenic region, with the ratios of 67.2360% and 62.6415%, respectively. Based on the phylogenetic tree constructed by the maximum likelihood method, the 19 samples could be divided into four categories. Among them, Y_10 and Y_38 were put into one category, while Y_2 was put into a separate category. These two were first differentiated from other cultivars and species. Similar conclusions can be drawn from the results of genetic structure and principal component analysis. This study provided sequence foundation for the identifying of the molecular marker and genotype of G. jasminoides. It also provided theoretical foundation for subsequent resource conservation and utilization, the genetic localization of important agronomical traits, and high-quality variety formulation and breeding.
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