Hepeng Li

The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a biodiversity hotspot for this genus. Using R. simsii as the reference genome, we generated 39.40 Gb of high-quality sequencing data with a Q30 score of 96.65% and a GC content of 39.63%, achieving an average alignment rate of 92.79%. Through stringent filtering (QD ≥ 2, MQ ≥ 40), we identified 14,048,702 genome-wide single nucleotide polymorphism (SNP), predominantly characterized by the mutation types T:A>C:G and C:G>T:A. The widespread R. simsii and R. simsii var. putuoense exhibited significant genetic diversity, whereas the low-altitude widespread R. molle and the endemic R. simiarum exhibited lower genetic diversity. Moderate genetic differentiation (F_st = 0.097) was observed between R. simsii and R. simsii var. putuoense, while substantial genetic differentiation was detected among the other Rhododendron species. Principal component analysis (PCA), combined with phylogenomic reconstruction, demonstrated that the Rhododendron genus can be stratified into six well-supported genetic clades. Furthermore, this study provides the first genomic validation of the sibling relationship between R. simsii and its variety, R. simsii var. putuoense, and clarifies the systematic position of R. huadingense, suggesting that it should be classified as a new subgenus. This study establishes ddRAD-seq as a cost-effective tool, providing both a theoretical framework for SNP-based phylogenetics and critical insights for conserving China’s azalea biodiversity.

The mitochondrial genome of Spartina alterniflora, an invasive species with significant ecological and economic impacts, was analyzed to provide a theoretical basis for understanding its phylogenetic relationships and molecular biology. Mitochondrial genome sequences of S. alterniflora and 23 related species from NCBI were utilized for bioinformatics and comparative genomic analyses. A sliding window analysis identified three genes (rps2, atp9, and nad6) as potential DNA barcodes for species identification. Intracellular gene transfer (IGT) events between mitochondrial and chloroplast genome were detected, highlighting the dynamic nature of genomic evolution. A selective pressure analysis revealed that most protein-coding genes (PCGs) underwent purifying selection (K_a/K_s < 1), while the nad2 and ccmB genes showed signs of positive selection pressure (K_a/K_s > 1), indicating their role in adaptation. A phylogenetic analysis demonstrated a close relationship between S. alterniflora and Eleusine indica, supported by a collinearity analysis, which suggests environmental convergence. This study provides novel insights into the structural and evolutionary characteristics of the S. alterniflora mitochondrial genome, offering valuable genomic resources for future research on invasive species management and evolutionary biology.

The genetic characteristics of postintroduced Metasequoia glyptostroboides from three forest areas in Ningbo Forest Farm, China, were analyzed by using polymorphic SSR markers. High genetic diversity at the species level (N_a = 5.306, N_e = 3.411, I = 1.269, H_o = 0.604 and H_e = 0.640) was detected. No significant difference in diversity was observed between mother trees and seedlings, indicating random mating or the absence of a founder effect. The group with the highest diversity was Shangliang seedlings (SLGS). Inbreeding was detected in two groups (SLGM and LXS), possibly due to biased sampling and selective pressures on these groups. AMOVA disclosed most genetic variation within groups (88%), with moderate differentiation (F_st = 0.117) and some gene flow (N_m = 1.887) between groups. Population structure analysis classified the six groups into distinct units, highlighting the need for tailored conservation strategies. These findings inform conservation and management practices for the introduced M. glyptostroboides.

Acorus calamus, a perennial emergent herb, is highly valued for its ornamental appeal, water purification ability, and medicinal properties. However, there is a significant contradiction between the rapidly increasing demand for A. calamus and the diminishing wild resources. Understanding its geographical distribution and the influence of global climate change on its geographical distribution is imperative for establishing a theoretical framework for the conservation of natural resources and the expansion of its cultivation. In this study, 266 distribution records of A. calamus and 18 selected key environmental factors were utilized to construct an optimal MaxEnt model via the ENMeval package. We simulated the potential geographical distributions under current conditions and under three different climate scenarios (SSP126, SSP370, and SSP585) in the 2050s, 2070s, and 2090s. Additionally, we employed the jackknife method and response curves to identify the environmental factors with the greatest influence on the distribution of A. calamus, and their response intervals. The results indicate that the regularization multiplier (RM) of 3.5 and the feature combinations (FC) of linear (L), quadratic (Q), hinge (H), and product (P) are the optimal model parameter combinations. With these parameters, the model predictions are highly accurate, and the consistency of the results is significant. The dominant environmental factors and their thresholds affecting the distribution of A. calamus are the precipitation of the wettest month (≥109.87 mm), human footprint (≥5.39), annual precipitation (≥388.56 mm), and mean diurnal range (≤12.83 °C). The primary land use types include rivers and channels, reservoirs and ponds, lakes, urban areas, marshes, other constructed lands, rice fields, forested areas, and shrublands. Under current climate conditions, the suitable geographical distribution of A. calamus in China is clearly located east of the 400 mm precipitation line, with high- and low-suitability areas covering 121.12 × 10⁴ km², and 164.20 × 10⁴ km², respectively. Under future climate conditions, both high- and low- suitability areas are projected to increase significantly, whereas unsuitable areas are expected to decrease, with the centroid of each suitability zone shifting northward. This study provides a theoretical foundation for sustainable utilization, future production planning, and the development of conservation strategies for wild germplasm resources of A. calamus.