Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus, and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA–BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus. The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso. Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus.

Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.

High levels of intra-specific polymorphism and frequent hybridisation make it difficult to define species and correctly apply their scientific names. Populus L. is a challenging genus with plentiful natural and artificial hybrids. This study is a part of the project ‘Flora of Pan-Himalaya’ and aims to determine the taxonomic identity of P. gonggaensis N. Chao & J.R. He and to find out whether it is of hybrid origin. Whole-genome sequencing data were obtained from 57 samples. The SNP matrix was developed for phylogenetic reconstruction, ABBA-BABA statistics, PCA and ADMIXTURE analysis. The results indicate that P. gonggaensis is a spontaneous hybrid between P. lasiocarpa and P. cathayana. This study points out the importance of SNP data and comprehensive analyses for discovering the potential interspecific hybridisation and clarifies the usage of the name. In addition, the lectotype of P. gonggaensis was designated.

As the most diverse genus of Salicaceae, Salix is primarily distributed in the temperate zone of the Northern Hemisphere, encompassing 350–500 species worldwide. The genus’s evolutionary history is complex due to significant genetic differentiation. Chloroplast genes, being highly conserved, serve as effective tools for studying uniparental inheritance and evolution. In this study, we sequenced and assembled the chloroplast genomes of five representative Salix species. Phylogenetic relationships were constructed using chloroplast genome data, and structural differences among lineages were compared. These Salix chloroplast genomes exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. We successfully annotated 131 genes, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I showed higher variability in the SSC region, identifying five highly variable regions: petA-psbJ, rps16-rps3, ndhD, ccsA-ndhD, and ndhG-ndhI. Two rapidly evolving genes, ndhI and ycf4, were also identified. The total length of insertions and deletions (InDels) in Clade I was 1046 bp. Clade II exhibited greater variability in the LSC region, with four highly variable regions being identified: trnK-trnQ, ndhC-trnV, trnV, and psdE-petL. Four rapidly evolving genes—infA, rpoC1, rps18, and ycf1—were identified. The total length of InDels in Clade II was 1282 bp. Therefore, this study elucidated the chloroplast genome evolution across different Salix lineages, thereby providing deeper insights into intrageneric phylogenetic relationships.