Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.

Lilium henrici Franchet, which belongs to the family Liliaceae, is an endangered plant native to China. The wild populations of L. henrici have been largely reduced by habitat degradation or loss. In our study, we determined the whole chloroplast genome sequence for L. henrici and compared its structure with other Lilium (including Nomocharis) species. The chloroplast genome of L. henrici is a circular structure and 152,784 bp in length. The large single copy and small single copy is 82,429 bp and 17,533 bp in size, respectively, and the inverted repeats are 26,411 bp in size. The L. henrici chloroplast genome contains 116 different genes, including 78 protein coding genes, 30 tRNA genes, 4 rRNA genes, and 4 pseudogenes. There were 51 SSRs detected in the L. henrici chloroplast genome sequence. Genic comparison among L. henrici with other Lilium (including Nomocharis) chloroplast genomes shows that the sequence lengths and gene contents show little variation, the only differences being in three pseudogenes. Phylogenetic analysis revealed that N. pardanthina was a sister species to L. henrici. Overall, this study, providing L. henrici genomic resources and the comparative analysis of Lilium chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Lilium, molecular barcoding in population genetics.

We isolated Tamdy virus (TAMV; strain XJ01/TAMV/China/2018) from Hyalomma asiaticum ticks infesting Bactrian camels in Xinjiang, China, in 2018. The genome of the strain showed high nucleotide similarity with previously described TAMV strains from Asia. Our study highlights the potential threat of TAMV to public health in China.

Nomocharis pardanthina Franchet (Liliaceae) is an endangered species naturally distributed in China. The complete chloroplast genome sequence of N. pardanthina was generated by de novo assembly using whole genome next generation sequencing data. The chloroplast genome of N. pardanthina was 152,718 bp in length and divided into four distinct regions, such as large single copy region (82,154 bp), small single copy region (17,524 bp) and a pair of inverted repeat regions (26,520 bp). The genome annotation predicted a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that N. pardanthina is nested in Lilium and has close relationship to L. bakerianum and L. taliense.

C. macrophylla and C. tangutorum, collectively known as Shigecai in Chinese, are consumed as special and nutritious vegetables by the Tibetan, Qiang, and Yi communities in China. However, due to the insufficient knowledge of their phytochemical compositions and health benefits, the industrial utilization of these species in the food sector remains limited. Although Shigecai leaves contain substantial pectic polysaccharides, their chemical structures and biological activities remain unknown, which ultimately restricts their industrial utilization. Thus, to address this gap, this study systematically analyzed the chemical characteristics and biological functions of rhamnogalacturonan-I (RG-I)- enriched pectin from C. tangutorum (CTHDP) and C. macrophylla (CMHDP) leaves. The results demonstrate that Shigecai leaves are promising sources of RG-I-enriched pectin, with yields of 57.63–65.21 mg/g dry weight. In addition, both CTHDP and CMHDP exhibited highly similar chemical and structural properties, dominated by RG-I and homogalacturonan (HG) pectin regions, with RG-I ratios of 60.14–63.33 mol%. Furthermore, both samples demonstrated notable antioxidant ability, antiglycation activity, prebiotic potency, and immunoregulatory effects, which were strongly linked to their bound polyphenol content, uronic acid content, and molecular weight. These findings support the industrial utilization of Shigecai and establish Shigecai-derived RG-I-enriched pectin as a promising functional food ingredient.

Investigating geological and climatic shifts in the Himalayan-Hengduan Mountains (HHM) and Qinghai-Tibet Plateau (QTP) is vital for unraveling environmental impacts on biogeography and evolution. We analyzed the evolutionary history of 3 Notholirion species across these regions, studying 254 individuals from 31 populations using 5 chloroplast DNA markers (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG) and nuclear ITS. A total of 1,145 low-copy nuclear genes (LCGs) and 112 chloroplast genes from 11 representative individuals were further utilized for phylogenetic reconstruction. Divergence timing was estimated with 147 plastomes, including 10 Notholirion populations. Fourteen cpDNA and 27 ITS haplotypes revealed species-specific variation. Phylogenetic analyses confirmed a monophyletic origin for all 3 species, with population-level nested relationships and cytonuclear discordance attributed to incomplete lineage sorting (ILS) and hybridization. Dating and ancestral reconstruction traced Notholirion’s origin to the southern Himalayas during the Late Oligocene (25.05 Ma), with diversification commencing in the Late Pliocene (7.43 Ma). MaxEnt modeling indicated stable species distributions from the Last Interglacial to future projections. The initial split of Notholirion was triggered by climate changes following the uplift of the QTP. Subsequently, dramatic climatic fluctuations during the Pleistocene and the complex topography of the HHM region jointly promoted species dispersal and diversification, ultimately shaping its current biogeographic distribution and phylogenetic structure. High genetic diversity likely stems from prolonged evolutionary history, sexual reproduction, and habitat fragmentation. The high genetic differentiation observed among Notholirion populations may be attributed to pronounced environmental changes across their distribution range, along with limited seed production and dispersal capacity.