Phylogenomics of the genusPopulusreveals extensive interspecific gene flow and balancing selection

Abstract

Summary Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.

Evidences for a role of two Y-specific genes in sex determination in Populus deltoides

“…P. deltoides belongs to subgenus Aigeiros in the genus Populus . To test whether the hemizygous YHS1 region is present in other poplars, we sequenced the genome of a male P. davidiana , in the same subgenus, Leuce , as P. tremula and P. tremuloides (in an earlier-branching section of Populus than Aigeiros 44 ); sex-determining regions of all three subgenus Leuce species map to the pericentromeric region of chromosome XIX 17 , 29 . Coverage analysis of genome sequences of 49 P. davidiana females and 47 males, using the male sequence as the reference, detected a 126 kb YHS on a contig (ctg345, Supplementary Fig.…”

A general model to explain repeated turnovers of sex determination in the Salicaceae

“…Here, we identify the sex determination systems of two additional Populus species, P. euphratica and P. alba , which are from sects. Turanga and Populus respectively (Wang et al , 2020). We report their complete SDR assemblies and propose a general model to illustrate the potentially shared mechanism of sex determination in this family.…”

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies

“…two Populus deltoides, one Populus angustifolia, and one Populus fremontii individuals for comparison. These species are closely related to P. trichocarpa and co-occur naturally in some parts of its natural range (Wang et al, 2019). These four species therefore hybridize naturally with P. trichocarpa.…”