Comparative plastome analysis and phylogenetic relationships of Chinese Myricaria species (Tamaricaceae)
TL;DR
Overall, Myricaria plastomes show a pattern of highly conserved genome structure coupled with localized sequence divergence, providing valuable resources for phylogenetic resolution, species identification, and plastome evolutionary studies.
Abstract
The genus Myricaria (Tamaricaceae) comprises shrubs widely distributed across arid and high-altitude regions of Eurasia, with China representing an important diversity center, particularly in the Qinghai–Tibetan Plateau and adjacent areas. To investigate plastome evolution and phylogenetic relationships within this genus, we sequenced and comparatively analyzed complete plastomes of five Myricaria species from China, together with those of Reaumuria as an outgroup. All plastomes exhibited a typical quadripartite structure and highly conserved gene composition, containing 127–135 genes, indicating strong structural stability across the genus. Despite the overall conservation of plastome architecture, minor size differences were observed and were mainly associated with contraction and expansion of inverted repeat (IR) boundaries. Comparative analyses revealed heterogeneous patterns of sequence divergence, with nucleotide variation primarily concentrated in intergenic regions and a limited number of protein-coding genes, whereas IR regions showed relatively high conservation. Simple sequence repeats (SSRs) and long repeats displayed species-specific distribution patterns, contributing to localized plastome variation. Sliding window analysis identified several mutation hotspots mainly located in single-copy regions, suggesting their potential utility for species identification and phylogenetic studies. Phylogenomic analyses based on complete plastome sequences strongly supported the monophyly of Myricaria and resolved major relationships among sampled species. However, limited resolution among some closely related taxa suggests recent diversification and possible incomplete lineage sorting. Overall, Myricaria plastomes show a pattern of highly conserved genome structure coupled with localized sequence divergence, providing valuable resources for phylogenetic resolution, species identification, and plastome evolutionary studies.