Zhaoping Yang

Tamarix species play a significant ecological role in desert transformation and climate improvement, representing nearly 75% of Tamaricaceae. However, due to their high morphological variability and susceptibility to interspecific hybridization, Tamarix remains one of the most poorly classified genera among flowering plants, which has significantly impeded the utilization of Tamarix species in ecological restoration projects across desert regions. China is among the countries most severely affected by desertification. Therefore, this study aims to compare chloroplast genomes among Tamarix species distributed in China, clarify their phylogenetic relationships, and identify molecular markers for species identification. In this study, we obtained the complete chloroplast genomes (CPGs) of 16 Tamarix species (33 CPGs), 24 of which were newly generated. A total of 1,650 non-SSR-related indels and 1,428 non-indel-related SSRs were identified, with mononucleotide SSRs being the most abundant. Comparative analyses using mVISTA revealed high sequence similarity across Tamarix chloroplast genomes, indicating strong conservation, except for Tamarix androssowii (OR619632). Overall, inverted repeat (IR) and coding regions were more conserved than single-copy and noncoding regions. Several intergenic regions showed higher variability than commonly used universal DNA markers. Phylogenetic analyses strongly supported the monophyly of Tamarix with two Myricaria samples as outgroups. Using 35 CPGs, we reconstructed a well-resolved phylogeny of Tamarix. Variations in branch lengths and support values provide new insights into intrageneric relationships within the genus. The genomic resources generated in this study offer a valuable foundation for future research on population genetics, species identification, and conservation of Tamarix.

Stachyurus , the sole genus of the Stachyuraceae family, comprises approximately 10 species distributed across eastern Asia, with potential applications in horticulture and medicine. However, limited genetic resources have hindered comprehensive research on this genus. Here, we sequenced and assembled the complete chloroplast genomes (cpDNAs) of 25 Stachyurus accessions, representing seven currently accepted species and one variety. The assembled Stachyurus cpDNAs range from 161,624 to 162,947 bp in length, with a GC content of 37.0–37.1% and 129–131 genes. Comparative analyses revealed a high degree of conservation in genome size, structure, inverted repeat (IR) boundary dynamics, GC content, and repeat patterns. Nevertheless, subtle variations driven by IR boundary shifts, gene loss (particularly ycf15 ), and differences in long sequence repeats collectively account for the observed cpDNA length variation. Seven hypervariable regions as promising molecular markers and four genes exhibited signatures of positive selection were identified. Phylogenetic analyses based on complete cpDNAs showed widespread paraphyly and strong cytonuclear discordance with previous nuclear phylogenies, providing clear evidence of chloroplast capture associated with hybridization. While reciprocal monophyly between Chinese and Japanese species was supported, relationships within the Chinese clade remain poorly resolved. These findings underscore the limitations of plastid data alone and highlight the urgent need for integrative studies combining nuclear genomic data, dense population sampling, and morphological/ecological information to clarify species boundaries and taxonomic relationships within Stachyurus . This study provides essential chloroplast genomic resources for future phylogenetic, phylogeographic, and adaptive evolution research on this understudied genus.

During an extensive botanical survey in Ulugqat Township, Wuqia County, Xinjiang, China—a region along the country’s western border that remains significantly understudied— Astragalus wuqiaensis , a new species in Astragalus sect. Cenantrum (Fabaceae) was discovered. This perennial herb is characterized by its free stipules, yellow flowers, lax racemes, a long-stipitate ovary, and membranous fruit valves, aligning with the diagnostic features of sect. Cenantrum and supporting its placement therein. It differs from other sect. Cenantrum members by its markedly smaller leaflets (2–8 mm × 2–5 mm). Phylogenetic analysis of nrITS sequences provides robust support for its sectional affiliation (BS = 94%, PP = 1). A detailed morphological description, diagnostic illustrations, and habitat information are provided to confirm its novelty.

The family Caryophyllaceae has traditionally been divided into three subfamilies (i.e. Alsinoideae, Caryophylloideae, Paronychioideae). However, the monoph

In desert plants, outcrossing is frequently limited by pollinator scarcity, leading to a certain percentage of self-fertilization. However, research on the ecological adaptations of self-fertilized seeds remains limited. Gymnocarpos przewalskii Maxim, a Tertiary relict plant in the arid deserts of Northwest China, exhibits pronounced self-pollination. In this study, the population of G. przewalskii from the fifth regiment of Alar City was selected to explore its self-pollination types, self-pollination percentages, and ecological adaptations. We found that artificially cross-pollinated G. przewalskii produced heavier seeds, faster germination, seedlings with greater biomass, and stronger environmental adaptability than self-pollination. However, the frequency of insect visits per flower was less than one. The fruit setting rate of natural pollination was 6.90%, while that of self-pollination was 4.43%, accounting for 64.20% of the natural fruit setting rate. Additionally, G. pzewalskii’s filaments elongated rapidly to make the anthers and stigma at the same height before flowering. These characteristics suggest that G. przewalskii is capable of autonomous self-pollination and is prior selfing. Gymnocarpos przewalskii likely produces a high proportion of the selfing merely to ensure population survival. These findings offer valuable insights into the adaptation of desert plants to the scarcity of pollinators.

Ferula sinkiangensis K.M. Shen is a threatened medicinal plant endemic to Xinjiang, China, with a small population size and a narrow distribution range. We assessed the status of this species with respect to its population age structure, the level of threat and extinction risk. Only one population remains, in Yining County, Xinjiang. We conducted field surveys of the population in 2022 and 2023, counting 2,033 and 1,515 individuals, respectively, in 144 sample quadrats. We assessed the age structure of the population by counting the number of basal leaves of each individual. The frequency distribution had an inverted J-shape, indicative of a relatively stable age structure. However, the number of mature individuals was small, raising concerns about the risk of genetic drift and inbreeding. This species is also threatened by habitat destruction and inappropriate collection practices. We recommend that F. sinkiangensis is categorized as Critically Endangered on the IUCN Red List on the basis of criteria B2ab(iii), C2a(i) and D.

Background: Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods: A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results: The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (F_ST = 0.521). The mean value of gene flow (N_m) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.

Introduction: Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families.MenispermumL. (Menispermaceae) consists of three species,M. dauricumDC.,M. canadenseL., andM. mexicanumRose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whetherM. mexicanumis a distinct species, a variety ofM. dauricum, or simply a synonym ofM. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.Methods: In this study, we examined phylogenomics and phylogeography ofMenispermumacross its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships ofMenispermumand explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.Results and discussion: Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show thatMenispermumclusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense+M. mexicanum). However,M. mexicanumis nested withinM. canadenseand, as a result, we support thatM. mexicanumis a synonym ofM. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK,ycf1), four introns (trnK intron,rpl16intron,rps16 intron,ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA,ndhF-rpl32,trnK-rps16, andtrnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai–Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.