Transcriptome data analysis provides insights into the conservation of Michelia lacei, a Plant Species with Extremely Small Populations distributed in Yunnan Province, China

Abstract

Abstract Background Michelia lacei W.W.Smith (Magnoliaceae) is an evergreen tree with high ornamental and scientific value. It was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both 2012 and 2021, due to the extremely small population size and narrow geographical distribution. Currently, research on M. lacei is limited to assessing the conservation status and population ecology, and to date there is no population genetics study. In this study, transcriptome data analysis was conducted on a total of 64 individuals from 7 populations of wild and cultivated M. lacei, resulting in the generation of 104,616 single-nucleotide polymorphisms (SNPs) that can be used in subsequent analyses. Results The population structure of M. lacei was analyzed using three methods, and the existing populations could be divided into three genetic clusters. In an analysis of population genetic diversity, the average π, HO, HE, FIS, and Tajima's D calculated across all populations were 0.298, 0.190, 0.702, 0.358, and 1.090, respectively. The population dynamics also reflected population changes in M. lacei during two past glaciations. The population size is thought to have stabilized about 10,000 years ago, however, there are now only 52 individuals of M. lacei known from the wild in China. Environmental changes have also promoted adaptive evolution of the species, as analysis of outlier loci indicates that some populations have high potential to adapt to the adverse environments, providing valuable genetic resources for the conservation of this species. Conclusions Our study clearly reveals the genetic background of M. lacei in different populations and the genetic diversity among the populations. Past gene flow between populations also reflects the causes of the current genetic structure. Combining inference of population history and adaptive analysis of M. lacei provides new insights into the conservation of genetic resources and facilitate the recovery of population size in this threatened plant species.