In the current context of climate change, the Western Himalayas are thought to be warming faster than the global average rate. Despite this rapid warming, our understanding of alpine vegetation composition and the underlying factors shaping its patterns in the Western Himalayan alpine highlands of Pakistan remains limited. Extensive field sampling was conducted at 24 sites ranging in altitude from 3300 m to 4200 m. The entire altitudinal range was divided into three belts i.e., low-altitude sites, medium-altitude sites, and high-altitude sites (HAS). Results revealed that alpine flora consisted of 251 species (belonging to 51 families. The findings revealed that 83 of the 251 species evaluated contributed significantly to the change in species composition between three altitudinal sites. The species that contributed the most to the variance in species composition between communities made up 75% of the total, demonstrating that these species are important in structuring plant communities at different altitudes. Among the alpine flora, a significant (49%) dominance was observed from nine families, comprising a total of 123 species. The largest family, Asteraceae, had the highest number of species, followed by Poaceae and Rosaceae. Hemicryptophytes emerged as the prevailing life form, while Microphylls were the dominant leaf type. Phytosociological Indices revealed that diversity levels decreased with increasing altitude, indicating a significant impact of altitude on plant diversity. Canonical correspondence analysis suggested that altitude, grazing, and soil erosion are important in explaining variance in plant distribution patterns in the alpine flora. Twelve indicator species were discovered in three different altitudinal groups. In the LAS, Bistorta affinis, Geranium himalayense, Poa nemoralis, and Sibbaldia cuneata, had a significant indicator value, whereas in the medium-altitude sites MAS Allium humile, Bistorta affinis, Juniperus communis, and Rhododendron campanulatum had significant p-values. In high altitude sites HAS, indicator plants were Bistorta affinis, Juniperus communis. Our results identified 51 vulnerable species with very low abundance values whereas 17 threatened species having extremely low (<0.1) abundance values are a vital conservation priority in the region. Results may be helpful to formulate immediate conservation management strategies to conservethe precious floristic wealth of the alpine Region.

Distribution patterns of alpine flora for long-term monitoring of global change along a wide elevational gradient in the Western Himalayas

Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism.We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening.Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies. 

A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes. 

Comparative Analyses of the Complete Mitogenomes of Two Oxyria Species (Polygonaceae) Provide Insights into Understanding the Mitogenome Evolution Within the Family

Abstract Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan‐Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax . We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax . Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax . 

Phylogenomic insights into species relationships, reticulate evolution, and biogeographic diversification of the ginseng genus Panax (Araliaceae), with an emphasis on the diversification in the Himalayan‐Hengduan Mountains

Phylogeography of Semenovia malcolmii, an endemic species on the Qinghai-Tibet Plateau

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Spatial distribution patterns and formation of global spermatophytes.

How species respond to ongoing climate change has been a hot research topic, especially with the controversy in shifting range (movement) or persisting in local habitat (in situ) as the primary response. Assessing the relative roles of range shifts, phenotypic plasticity and genetic adaptation helps us predict the evolutionary fate of species. We aim to explore the evolutionary strategies of plants under climate change from a keystone herb in alpine ecosystems, Mirabilis himalaica, along its elevational gradient.

Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya‐Hengduan Mountains across elevational gradients

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The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Spatial distribution patterns and formation of global spermatophytes.

Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya‐Hengduan Mountains across elevational gradients