The chromosome-scale genome and population genomics reveal the adaptative evolution of <i>Populus pruinosa</i> to desertification environment

Abstract

The <i>Populus pruinosa</i> is a relic plant that has managed to survive in extremely harsh desert environments. Owing to intensifying global warming and desertification, research into ecological adaptation and speciation of <i>P. pruinosa</i> has attracted considerable interest, but the lack of a chromosome-scale genome has limited adaptive evolution research. Here, a 521.09 Mb chromosome-level reference genome of <i>P. pruinosa</i> was reported. Genome evolution and comparative genomic analysis revealed that tandemly duplicated genes and expanded gene families in <i>P. pruinosa</i> contributed to adaptability to extreme desert environments (especially high salinity and drought). The long terminal repeat retrotransposons (LTR-RTs) inserted genes in the gene body region might drive the adaptive evolution of <i>P. pruinosa</i> and species differentiation in saline-alkali desert environments. We recovered genetic differentiation in the populations of the northern Tianshan Mountain and southern Tianshan Mountain through whole-genome resequencing of 156 <i>P. pruinosa</i> individuals from 25 populations in China. Further analyses revealed that precipitation drove the local adaptation of <i>P. pruinosa</i> populations via some genetic sites, such as MAG2-interacting protein 2 (<i>MIP2</i>) and SET domain protein 25 (<i>SDG25</i>). This study will provide broad implications for adaptative evolution and population studies by integrating internal genetic and external environmental factors in <i>P. pruinosa</i>.