Robust phylogenies and comprehensive taxonomies are fundamental for understanding the evolution and classification of species-rich genera. Corydalis (Papaveraceae), comprising approximately 530 species, is one of the largest and most diverse angiosperm genera. While a recent classification system has been established based on phylogenomic and morphological evidence, it relied primarily on plastid genomic data, with limited consideration given to nuclear genes. Here, we compiled the genome skimming data from 411 accessions representing 265 species covering all recognized 39 sections of Corydalis. Using 6617 high quality nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs), we reconstructed a comprehensive phylogenetic framework for Corydalis. Our results strongly supported the division of Corydalis into four subgenera, including subg. Cremnocapnos, subg. Bipapillatae, subg. Sophorocapnos, and subg. Corydalis. Of the 33 sections sampled with multiple species, ten were recovered as non-monophyletic, including sect. Cheilanthifoliae, sect. Thalictrifoliae, sect. Vermiculares, sect. Rupifragae, sect. Asterostigmata, sect. Mucronatae, sect. Elatae, sect. Fasciculatae, sect. Flexuosae, and sect. Bimaculatae. Phylogenetic network analyses revealed pervasive hybridization and introgression in subg. Corydalis, suggesting that widespread hybridization and introgression are major drivers of both phylogenetic discordance and sectional non-monophyly. Our study not only provides a critical nuclear genomic perspective for Corydalis, but also offers concrete guidance for refining its infrageneric classification. In addition, our findings also underscore the necessity of future studies that integrate expanded sampling, high-quality genetic markers, and morphological data to resolve the classification of taxonomically problematic sections.

Globally, the Acidobacteriota phylum is both extraordinarily widespread and abundant, serving indispensable roles in carbon, sulfur, and nutrient cycling. However, our comprehension is marked by a significant culture-based bias. Many of the newly reconstructed metagenome-assembled genomes (MAGs) represent uncultured lineages that remain substantially understudied, highlighting this gap. Concurrently, research on Acidobacteriota has been predominantly focused on soil environments, with a scarcity of studies in other environments. Here, we bridged this gap by compiling a genomic catalog of 4317 genomes. Protein content analysis, in conjunction with large-scale metabolic reconstructions, delineates seven genomic clusters of Acidobacteriota with unique metabolic profiles. Clusters 1 and 2 are soil-preferring, and clusters 3, 4, and 6 from various environments, exhibit diverse energy metabolism, including aerobic, facultatively anaerobic, anaerobic, and fermentative processes, and utilize a wide range of carbon substrates. Conversely, aquatic-preferring cluster 5 and various environments derived cluster 7 are strictly anaerobic, relying on nitrate/nitrite reduction or fermentation, and cluster 5 have a limited carbon utilization range. Our analyses have also identified previously unrecognized roles in C1 metabolic pathways, Calvin cycle, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification among the uncultured Acidobacteriota, indicating that Acidobacteriota represent overlooked important function involved in methylotrophy, CO oxidation, carbon fixation and nitrogen cycling. These findings provide new insights into the metabolic diversity of Acidobacteriota, emphasizing their functional importance across diverse taxa and environments, and significantly expanding our understanding of these dominant yet understudied bacteria.

The green odorous frog (Odorrana margaretae) represents an excellent model system for investigating the genetic basis of anuran skin secretions. Here, we report a chromosome-level genome assembly comprising 13 chromosomes with a total size of 6.20 Gb. Within this large genome, approximately 4.78 Gb (77.01%) consists of repetitive elements, with evidence of recent rapid expansions of DNA transposons and long terminal repeats (LTRs). Comparative gene family analyses identified 154 significantly expanded gene families in the green odorous frog, predominantly associated with innate immune functions. Targeted data mining revealed a diverse repertoire of antimicrobial peptides (AMPs), characterized by a massive expansion of histone-derived AMP copies organized into large tandem clusters. Additionally, the genome harbors an extensive array of olfaction-related genes, including 1,035 functional olfactory receptor (OR) genes, with notable expansions in the α and γ subfamilies responsible for detecting airborne odors; transposable elements (TEs) are significantly enriched in the flanking regions of these OR genes. The species also exhibits a signature of tandem duplication in trace amine-associated receptor 2 (TAAR2) genes. Collectively, these findings suggest enhanced capabilities in odor detection and chemical communication, likely linked to its skin secretions. This high-quality reference genome provides a foundation for future studies on the genetic regulation of potent skin secretions in this species and other amphibians.

Orostachys is a small genus in the family Crassulaceae with about 16 species, the majority of which are biennial herbs. The taxonomic boundaries and phylogenetic relationships between Orostachys and its allied genera have been controversial, partly because of the absence of a robust phylogenetic framework. In the present study, we collected 30 samples, representing 27 species of Orostachys and related taxa. Using Hyb-seq and genome skimming methods, we obtained 750 single-copy orthologous nuclear genes and all plastid protein-coding genes. Both nuclear and plastid phylogenies revealed the polyphyly of Orostachys s.l., comprising three independent lineages corresponding to Kungia (= O. sect. Schoenlandia), the O. spinosa clade (= O. subsect. Appendiculatae) and the O. malacophylla clade (= O. subsect. Orostachys). These lineages each formed sister relationships with their respective allied taxa: Kungia with Sinocrassula, the O. malacophylla clade with Hylotelephium, and the O. spinosa clade with Meterostachys. Minimal gene flow was detected among the three lineages, and between each lineage and its sister group, indicating well-established reproductive isolation. Morphological character analyses corroborated these phylogenomic findings. Our results: (1) support Fu's taxonomic treatment of O. sect. Schoenlandia as the independent genus Kungia; (2) do not support merging O. subsect. Orostachys (= the O. malacophylla clade) with Hylotelephium; and (3) suggest that O. subsect. Orostachys should be taxonomically recognized as a new genus Amblystachys and make the relevant new combinations.

Dalbergia (Leguminosae) is a pantropical genus that serves as an ideal system for studying pantropical biogeography and diversification. However, limited taxon sampling and molecular data have hindered the resolution of intrageneric relationships and understanding of its evolutionary history. Here, we reconstruct a densely sampled phylogeny of Dalbergia based on hybrid capture of 89 low-copy nuclear loci, including 98 species spanning all major biogeographic regions and most previously recognized taxonomical clades. Phylogenetic analyses using concatenated and coalescent approaches support the monophyly of Dalbergia and consistently identify six major clades, including a distinct and newly identified Africa-Madagascar lineage (clade E) with potential taxonomic significance. Our results propose merging two of its sections, sect. Dalbergia and sect. Selenolobium, and expanding sect. Ecastaphyllum to include some African species. Topological incongruences observed between concatenated and coalescent trees, together with the high gene tree conflict at certain nodes, are consistent with localized effects of hybridization and/or incomplete lineage sorting. Divergence dating and model-based biogeographic analyses support a Neotropical origin of Dalbergia in the middle Eocene (~39 Ma), followed by repeated long-distance dispersal events from Africa to Asia, Neotropics, and Madagascar, and back into the Neotropics. An early diversification burst in Africa during the late Oligocene–early Miocene (~27–18 Ma) preceded the genus’s intercontinental expansion. Diversification rates are high across all four regions, with Madagascar showing the highest speciation rate. These macroevolutionary dynamics coincided with Eocene–Miocene climatic changes and habit shifts. This study provides a robust phylogenetic framework for Dalbergia, refines its temporal and biogeographic history, and illustrate how dispersal, climatic change, and lineage-specific diversification have interacted to generate pantropical biodiversity.

Conifers only have about 670 species worldwide but are one of the ecologically and economically most important plant groups. Their current distributions resulted from the interplay of speciation, dispersal and extinction, with some major clades restricted to the Northern Hemisphere whereas others are restricted to the Southern Hemisphere. Here, we explore global geographic patterns of mean diversification rate (MDR), representing recent speciation dynamics, within genera of conifers, and relate MDR to regional species richness and climatic conditions. We find that MDR is negatively correlated with species richness and latitude at a global scale; that latitudinal patterns and relationships of MDR to climatic factors differ between the Northern and Southern Hemispheres; that MDR is correlated positively with mean annual temperature and negatively with annual precipitation; that temperature-related variables explain less variation in MDR than precipitation-related variables in the Northern Hemisphere but more variation in the Southern Hemisphere; and that climate extreme variables explain more variation in MDR than climate seasonality variables. These patterns differ in many important details from those seen in angiosperms. We hypothesize that small land surface area and the associated paucity of broadly fragmented habitats may limit speciation in the wind-dispersed conifers, which requires broad spatial separation between diverging populations. Furthermore, conifer diversification peaks in arid habitats, probably related to numerous anatomical, physiological, and life strategy traits. Such differences between conifers and other major groups of land plants allow us to infer generalities of how geographic and climatic drivers and life history traits interact to determine the diversification dynamics of plants.

Chenopodiaceae s.s. (Amaranthaceae s.l.) contains the largest number of C₄ species among eudicots. Despite this, plastome evolution within this family has been investigated in only a few species. Here, we analyzed 119 plastomes from 115 species, including 78 newly sequenced plastomes, representing all subfamilies and most C₄ lineages of Chenopodiaceae s.s.. Plastome structural variants, rearrangements, and codon usage bias were compared across subfamilies and photosynthetic types. Multiple phylogenetic approaches were employed to reconstruct the evolutionary relationships within Chenopodiaceae s.s., and Bayesian divergence time estimation was performed. Various Mk models for discrete character evolution were tested to investigate the evolution of C₄ photosynthesis, and stochastic character mapping simulations were used to reconstruct shifts in photosynthetic pathways through time. Several plastome structural variants and rearrangements were identified, but associations with photosynthetic types were observed only in the subfamily Suaedoideae. Codon usage bias analysis revealed significant bias exclusively in C₄ species, suggesting enhanced translational efficiency and accuracy as an adaptation to environmental conditions. We inferred multiple independent origins of the C₄ pathway, with the oldest lineages—Bienertia (Suaedoideae) and Caroxyleae (Salsoloideae)—dating to approximately 34 and 32 million years ago (Ma), respectively, during the Oligocene. A marked increase in the number of C₄ lineages occurred between 20 and 15 Ma. Declining atmospheric CO₂ concentrations, combined with genetic, ecological, and environmental factors, likely promoted the expansion of C₄ photosynthesis until recently. Finally, we identified five new hypervariable regions that will be valuable for phylogenetic and DNA barcoding applications in Chenopodiaceae s.s..

Crataegus L. (hawthorns) is a taxonomically challenging genus within the Rosaceae family, exhibiting extensive morphological variation, frequent hybridization, and polyploidy. In China, about 18 species are currently recognized, but their subgeneric classification and species boundaries remain unresolved. To clarify these relationships, we analyzed 481 nuclear genes, 73 plastid coding sequences, and a comprehensive plastome dataset for 17 Chinese Crataegus species. Phylogenomic analyses of both nuclear and plastid data yielded well-supported trees that refine the taxonomy and elucidate evolutionary relationships within the genus. All Chinese species are resolved within two subgenera, C. subg. Crataegus and C. subg. Sanguineae, although most currently recognized species are not monophyletic, reflecting complex reticulate evolution involving hybridization and polyploidy. Integrating phylogenomic, morphological, and cytological evidence, we provide an updated taxonomic synopsis of Chinese Crataegus, describe one new species, propose five new combinations, and designate 31 lectotypes. This study establishes a robust framework for future systematic, conservation, and horticultural research on this ecologically and economically important lineage.