Crucihimalaya himalaica , a close relative of Arabidopsis and Capsella , grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata , from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica ’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica , might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.

Hippophae tibetana, belonging to the Elaeagnaceae family, is an endemic plant species of the Qinghai–Tibet Plateau, valued for its remarkable ecological restoration capabilities, as well as medicinal and edible properties. Despite being acknowledged as a useful species, its mitochondrial genome data and those of other species of the Elaeagnaceae family are lacking to date. In this study, we, for the first time, successfully assembled the mitochondrial genome of H. tibetana, which is 464,208 bp long and comprises 31 tRNA genes, 3 rRNA genes, 37 protein-coding genes, and 3 pseudogenes. Analysis of the genome revealed a high copy number of the trnM-CAT gene and a high prevalence of repetitive sequences, both of which likely contribute to genome rearrangement and adaptive evolution. Through nucleotide diversity and codon usage bias analyses, we identified specific genes that are crucial for adaptation to high-altitude conditions. Notably, genes such as atp6, ccmB, nad4L, and nad7 exhibited signs of positive selection, indicating the presence of unique adaptive traits for survival in extreme environments. Phylogenetic analysis confirmed the close relationship between the Elaeagnaceae family and other related families, whereas intergenomic sequence transfer analysis revealed a substantial presence of homologous fragments among the mitochondrial, chloroplast, and whole genomes, which may be linked to the high-altitude adaptation mechanisms of H. tibetana. The findings of this study not only enrich our knowledge of H. tibetana molecular biology but also advance our understanding of the adaptive evolution of plants on the Qinghai–Tibet Plateau. This study provides a solid scientific foundation for the molecular breeding, conservation, and utilization of H. tibetana genetic resources.

Hippophae tibetana, one of the highest-altitude woody plants endemic to the Qinghai-Tibet Plateau, primarily thrives on riverbanks formed by glacial meltwater. As a dioecious species, it demonstrates significant ecological and economic value in extreme alpine environments. However, the lack of sex identification techniques outside of the flowering period severely limits research on sex ratio, differentiation, and breeding. There is an urgent need to develop effective sex-linked molecular markers that are independent of developmental stages, but current research in this area remains limited. This study developed a set of accurate sex-linked molecular markers for the rapid identification of male and female individuals of H. tibetana. Through whole-genome resequencing of 32 sexually differentiated H. tibetana samples, this study offers strong evidence supporting chromosome 2 as the sex chromosome and successfully identified key loci related to sex determination on this chromosome. Utilizing these loci, we, for the first time, developed three reliable pairs of sex-specific molecular markers, which exhibited high accuracy during validation across various geographic populations, offering an effective tool for the sex identification of H. tibetana. Additionally, this study lays the groundwork for further research into the mechanisms of sex determination and the evolution of sex chromosomes in H. tibetana.

Hippophae gyantsensis is a dioecious plant endemic to the Qinghai-Tibet Plateau and is significant for ecological restoration and sand stabilization. Its fruit is rich in bioactive compounds that offer economic potential. However, the inability to distinguish sexes before flowering and prolonged maturation hinder breeding and cultivation. We performed whole-genome resequencing on male and female plants, identified large insertion/deletion (InDel) variants, and developed two sex-specific primers (Higy_04 and Higy_06). These primers enable rapid, accurate PCR-based sex identification. All sex-specific sites were located on chromosome 2, suggesting its potential role as the sex chromosome. Additionally, we found a 1:1 sex ratio among offspring from the same mother plant, consistent with Mendelian inheritance, indicating that sex segregation is mainly genetically controlled. This work lays the foundation for developing molecular markers applicable across the entire genus Hippophae and contributes to understanding sex chromosome formation and adaptive evolution within the genus.

The Tibetan plateau, with complex and diverse ecosystems, is an important ecological security barrier to China. However, climate change and the spread of invasive plant species have imperiled the once pristine and diverse ecosystem of the region. To prevent the further spread and control of invasive plants, it is important to delineate the potential distribution patterns of alien invasive plants at the regional scale across Tibet and understand their responses to climate change. Galinsoga parviflora Cav., a member of the family Asteraceae, is an annual herbaceous plant distributed globally as an invasive weed and possesses characteristics that make it highly invasive, such as a strong ability to proliferate and disperse. The species is also known to have an allelopathic effect. There has been no report on the spatial distribution of G. parviflora in Tibet. Using field survey data, we investigated the risk of G. parviflora invasion and its impacts on the ecological safety of Tibet. We employed the MaxEnt model using the R language and SPSS software to optimize and select model parameters and data. We acquired various environmental variables along with current and future climate change scenarios (two carbon emission scenarios, SSP126 and SSP585, for the years 2050 and 2090) to predict the geographic distribution and potential risk areas in Tibet that G. parviflora can invade. The MaxEnt model accurately predicted the distribution of G. parviflora in Tibet with an average AUC of 0.985. The most suitable environmental conditions in which G. parviflora performed the best in Tibet included a mean annual temperature of 6.2–10.0 °C and an elevation range of 2672–3744 m above sea level. Our results indicate that low precipitation during the coldest quarter of the year (mean temperature −2–3 °C) was the most important variable predicting G. parviflora distribution. The results also showed that the species was hardly found when precipitation in the coldest quarter exceeded 155 mm. The current potential invasion risk areas for G. parviflora included the river valleys of central, southeastern, and eastern Tibet. With future climate change scenarios (i.e., SSP126, SSP585), the suitable habitats for G. parviflora distribution will likely shift to northwest regions from the southeast. Particularly under the highest carbon emission scenario (i.e., SSP585), the potential risk area expands more rapidly, and the center of distribution shifts to northwest regions. These findings provide useful information about the current and future changes in G. parviflora distribution in Tibet, which is crucial for the comprehensive and proactive management and control of G. parviflora under future climate change.

Introduction: Phlomoides rotata, an important Tibetan medicinal plant, has garnered significant attention due to its remarkable medicinal value and ecological functions. However, overharvesting and climate change have progressively reduced its distribution range, threatening its survival.Methods: This study employed an optimized MaxEnt model, integrating field survey data and multiple environmental variables, to predict and analyze the potential suitable distribution of P. rotata in Tibet.Results: The model achieved high predictive accuracy, with Ture skill statistic (TSS) = 0.87 and Cohen’s Kappa Coefficient (Kappa) = 0.81. Under current climatic conditions, the suitable habitat area of P. rotata is 33.31×10⁴ km², primarily distributed in alpine meadows and sparse shrublands in regions such as Lhasa, Nyingchi, Qamdo, Shannan, and eastern Nagqu. Analysis of key environmental factors revealed that land cover type (30.7%), temperature seasonality (19.9%), and vegetation type (10.2%) are the most significant drivers influencing the distribution of P. rotata. Under future climate change scenarios, the distribution of suitable habitats exhibits notable dynamic trends. In the low-emission scenario (SSP126), the suitable habitat area shows an overall expansion. In contrast, under medium- and high-emission scenarios (SSP245 and SSP585), the suitable habitat area gradually shrinks. The distribution centers consistently migrate northwestward, with the longest migration distance observed under SSP585 (89.55 km).Discussion: This study identifies the critical driving factors for the distribution of P. rotata and elucidates its response patterns to climate change. These findings provide a theoretical foundation for the resource management, ecological conservation, and sustainable utilization of Tibetan medicinal plants while offering valuable references for the study of other alpine plants.