Genetic relationship analysis of Paulownia species using whole genome re-sequencing

Based on the SNP markers developed by whole genome re-sequencing, the genetic relationship and population genetic structure of Paulownia species were analyzed, which will provide a theoretical basis for reveling the phylogenetic relationship and classification of Paulownia species.

11 species of Paulownia were sequenced using WGRS, and the basic quality and characteristics of the obtained data were evaluated. Using the whole genome sequence of Paulownia fortunei as the reference genome, the SNP markers with high quality were obtained. Principle component analysis (PCA) and the phylogenetic and genetic structure of these species were analyzed through VCF2Dis, MEGA11 and fastSTRUCTURE and other software. GO enrichment analysis was performed by the R package of cluster Profiler.

81.87% of the reads were mapped to the P. fortunei genome, and 7 492 966 SNPs were obtained after cleaning and filtering. Based on these SNPs, the genetic distance between each of the two species was estimated. The genetic distance ranged from 0.15 to 0.59, among which the distance between P. tomentosa and P. fortunei was the largest at 0.59, the distance between P. ichangensis and P. lampropylla, and the distance between P. albiphloea and P. lampropylla were the smallest as 0.15. The results of phylogenetic analysis, PCA, and genetic structure analysis confirmed that 11 species of Paulownia should be classified into 3 groups, which were the group of P. tomentosa(Ⅰ), the group of P. fargesii and P. taiwaniana(Ⅱ) and the group of P. fortunei, P. catalpifolia, P. lampropylla, P. albiphloea, P. ichangensis, P. kawakamii, P. jianshiensis and P. elonga(Ⅲ). Genes with high mutation rates were enriched to the cell wall-related pathway, pollen-related pathway, secondary metabolite-related pathway and morphogenesis-related pathway.

Using the WGRS technique to mine the SNP markers covering the whole genome, the genetic diversity and genetic structure of Paulownia species could be analyzed effectively. It lays a foundation for the systematic classification and efficient utilization of Paulownia germplasm resources.