Abstract
BACKGROUND: Stipa L., a genus of Poaceae, comprises over 150 species and is mainly distributed in Eurasia. Stipa species dominate the open grasslands and steppes in a variety of climates and habitats. The phylogenetic relationships within this genus are still controversial and unresolved. In this study, we sequenced and downloaded chloroplast genomes of 22 and 16 Stipa species, respectively. Subsequently, we conducted comparative analysis and constructed the phylogenetic tree using 38 plastid genomes (plastomes). RESULTS: Stipa chloroplast genomes demonstrated relatively conserved typical quadripartite structure, with length ranged from 137,120 bp to 137,859 bp. In total, the chloroplast genomes of Stipa species contained 131 genes, comprising 85 protein-coding genes, 38 tRNAs, and eight rRNAs. A total of 1,496 simple sequence repeats (SSRs) were identified and nine mutational hotspots were screened out, including psbA, psbZ-trnG-GCC, trnG-UCC-trnT-GGU, petN-trnC-GCA, rbcL, rpl16, ndhH, ndhF and rpl32. The phylogenetic tree revealed three strongly supported clades in Stipa. Species distributed in alpine grassland, such as Qinghai-Tibetan Plateau, consistently formed one clade. Stipa breviflora, S. przewalskyi and S. bungeana, distributed mainly in Loess Plateau, consistently formed another clade. In the third clade, the uncertain placement of subclades complicates the determination of the precise phylogeny within the genus Stipa. CONCLUSIONS: We reported the complete chloroplast genomes of 22 Stipa species and elucidated the structural characteristics of the chloroplast genome of 38 species of Stipa, and developed SSRs. Stipa species grouped into strongly supported clades within phylogenetic trees and were in accordance with their spatial distributions in Qinghai-Tibetan Plateau and Loess Plateau, respectively, though conflicts of species relationships demonstrated by topology among subclades were explored. The results indicate the importance of molecular markers for reconstructing the phylogeny of Stipa species. Our results illustrate the complex evolutionary history among the Stipa species in the eastern and central Eurasian steppe, which can be used to study the taxonomy, biogeography, diversification, evolution and origin of autochthonous species in the Eurasian steppe. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07487-6.