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

Abstract

The Populus pruinosa 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 P. pruinosa 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 P. pruinosa was reported. Genome evolution and comparative genomic analysis revealed that tandemly duplicated genes and expanded gene families in P. pruinosa 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 P. pruinosa 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 P. pruinosa individuals from 25 populations in China. Further analyses revealed that precipitation drove the local adaptation of P. pruinosa populations via some genetic sites, such as MAG2-interacting protein 2 (MIP2) and SET domain protein 25 (SDG25). This study will provide broad implications for adaptative evolution and population studies by integrating internal genetic and external environmental factors in P. pruinosa.

Acknowledgements

We would like to thank all authors for their valuable discussions. This work was financially supported by the Natural Science Foundation of China (32371838 and U1303101), the Bingtuan Science and Technology Program (2021BB010), and the Postgraduate Research and Innovation Project of Tarim University (TDBSCX202003).

Author contributions

J.H.S. performed investigation and writing-original draft. J.H.S. and J.D.X. performed formal analysis and visualization. C.Q., J.T.Z., S.H.Z., and X.Z. performed investigation. Z.H.W. performed project administration, acquisition of resources, and writing-review. Z.J.L. performed project administration, acquisition of resources, and funding acquisition. All authors revised and approved the final manuscript.

Data availability

The raw sequence reads (including short reads, long reads, and Hi-C reads) for the P. pruinosa genome, as well as the RNA-seq under salt and drought stress were submitted to NCBI (National Center for Biotechnology Information) with the BioProject accession number PRJNA863418. The assembly and annotation files were available from figshare (https://figshare.com/articles/online_resource/Pprgenome_fa/20705107/2). The whole-genome sequencing data for 156 P. pruinosa accessions also were uploaded to NCBI under the accession number PRJNA865525.

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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