Xueya Wei’s research while affiliated with Beijing Forestry University and other places

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.

Due to significant morphological differences and extensive interspecific hybridization, there are numerous species complexes with taxonomic challenges in the genus Populus. Integrative taxonomy, which combines evidence of morphology, molecular phylogeny, niche differentiation, and reproductive isolation, provides the most effective approaches for species delimitation. The Populus laurifolia complex, which belongs to Populus subg. Tacamahaca (Salicaceae), is distributed in the Altai Mountains and Tianshan Mountains. This complex exhibits morphological variability, making species delimitation challenging. Due to limited sampling and systematic studies, its taxonomy has remained unresolved. In this study, 337 specimens, along with online digital samples representing nearly all wild populations, were collected. Morphological analyses were performed to evaluate key traits and clarify species boundaries. Phylogenetic relationships were reconstructed using concatenation and coalescent methods based on 566,375 nuclear single-nucleotide polymorphisms (SNPs). Ecological niche differentiation was assessed, and ABBA–BABA analysis was used to examine interspecific hybridization. The results revealed that this complex, based on a series of significant character states, could be morphologically distinguished into three species—P. laurifolia (Populus pilosa considered a synonym of P. laurifolia), Populus talassica, and Populus pamirica—which also correspond to three well-supported clades in the phylogenetic trees. P. pamirica exhibits some degree of ecological niche differentiation from P. talassica and P. laurifolia, whereas the latter two show minimal differentiation. Gene flow within the complex remains limited. This research underscores the importance of integrating multiple lines of evidence in the classification of Populus, providing a framework for future taxonomic studies.

As the most diverse genus of Salicaceae, Salix is mainly distributed in the temperate zone of the northern hemisphere, with about 350 to 500 species worldwide. The evolutionary history of this genus is complicated because of the high genetic differentiation. Chloroplast genes are highly conserved, which makes it an effective tool for studying uniparental inheritance evolution. In this study, we sequenced and assembled five chloroplast genomes of representative species of Salix. The phylogenetic relationships of Salix were constructed using the chloroplast genome, and the differences in chloroplast structure among different lineages were compared. The chloroplast genomes of Salix exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. A total of 131 genes were successfully annotated, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I had higher variability regions in the SSC region, identifying 7 highly variable regions, namely ndhD, ndhF-trnL, trnL, ccsA-ndhD, ycf1, aptF, and aptF-rps14. The rapidly evolving clpP gene was identified. The deletion site of Clade I was 169 to 269 bp in length, and the insertion site was 183 to 283 bp in length. Clade II had higher variability regions in the LSC region, with four highly variable regions identified: ndhC-trnV, psdE-petL, clpP, and ccsA. The rapidly evolving rps18 and infA genes were identified. The deletion site of Clade II was 1703 to 2984 bp in length, and the insertion site was 1556 to 2837 bp in length. This study elucidated the evolution of chloroplast genomes across different lineages of Salix, offering deeper insights into the relationships within the genus.