Chloroplast genome-based genetic variation and genetic diversity of Ulmus pumila (Ulmaceae) germplasm

Abstract

Ulmus pumila is widely distributed in the north temperate zone and has timber and horticultural value. Assessing its genetic diversity could provide valuable insights into the levels and distribution of genetic variation in U. pumila resources, which could aid in the selection of representative and diverse germplasm. In this study, we sequenced the complete chloroplast genome of 51 U. pumila samples from 19 populations and investigated the population structure and genetic diversity of this species. The chloroplast genome of U. pumila exhibits the typical structure of angiosperm chloroplast genomes, characterized by a circular double-stranded structure. We identified 313 single nucleotide variants and 277 indels. Four markers, trnT-psbD, rpl32-trnL, rps16-trnQ, and the ndhA intron, had high variation in the chloroplast genome. Phylogenetic and population structure analyses showed that U. pumila could be divided into two major clusters, showing significant divergence between them. Furthermore, Cluster I was divided into three clades and Cluster II included two clades. The five clades diverged between 4 and 9 million years ago and the effective population size of U. pumila clades has remained relatively stable since the Pliocene, with no significant fluctuations observed. Our study revealed the genetic diversity and differentiation of U. pumila, providing valuable insights into its genetic variation and a basis for the effective conservation of germplasm resources.