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.

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.

The tribe Euphorbieae, the most species-rich lineage within the Euphorbiaceae family, comprises five genera across three subtribes (Anthosteminae, Neoguillauminiinae, and Euphorbiinae), with over 2000 species, predominantly in Euphorbia. While ecologically significant globally, critical gaps persist in resolving species-level phylogeny of Euphorbieae and elucidating the biogeographic drivers of its global distribution. Among the total 34 sampled species in Euphoroideae, 28 species were applied to represent all five genera in three subtribes of Euphorbieae, including ten newly sequenced species for all 11 extant species of Anthosteminae and Neoguillauminiinae, plus 18 representative Euphorbia (Euphorbiinae) species. Using plastome and nuclear ribosomal DNA (nrDNA) datasets, we reconstructed phylogenetic relationships, estimated divergence time, inferred ancestral areas, and analyzed diversification patterns. Our results strongly support Euphorbieae's monophyly and clarify sister relationships among subtribes. We present the first resolved species-level phylogeny for Euphorbieae (excluding the gigantic genus Euphorbia), revealing the tribe's evolutionary timeline, with instances of nuclear-plastid discordance suggestive of hybridization or incomplete lineage sorting. The crown age of Euphorbieae dates to approximately 62.11 million years ago (Ma) in the early Paleocene. Biogeographic analyses reveal the African origin at early Paleocene, followed by major dispersal events to Australasia, Asia, and the Neotropics. The combined plastome-nrDNA approach significantly enhanced phylogenetic resolution. These findings provide crucial insights into Euphorbieae's global 'out of Africa' distribution pattern, and contribute to understanding the role of key innovations and climatic shifts in plant diversification.

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.

Heliopora (subclass Octocorallia, order Scleralcyonacea, family Helioporidae), commonly known as the “blue coral”, represents the only reef-building lineage within Octocorallia. The genus shows diverse growth forms of branching, encrusting, and laminar types, which leads to ambiguities in traditional morphology-based taxonomy. Here, we investigated the diversity of Heliopora species in the South China Sea (SCS) and their phylogenetic relationships across the Indo-Pacific using integrated morphological and phylogenomic approaches. Whole-genome resequencing of 52 colonies from the SCS islands, combined with published data from 244 samples worldwide, revealed three distinct clades: H. coerulea, H. hiberniana, and a previously undescribed lineage. Morphological analyses characterized the new lineage with blue skeleton, short columnar to encrusting growth form, large autopores with 12–15 pseudosepta, absence of worm tubes, and elaborated coenchymal echinulations. These features contrast with the long-branching to lobate H. coerulea and the white-skeletoned H. hiberniana. Based on its unique morphology and distinct phylogenetic position, we describe this lineage as a new species, Heliopora chinensis sp. nov. It is distributed mainly in the SCS islands, Taiwan Island, and the Ryukyu Islands. Meanwhile, global research and citizen science records suggest that H. hiberniana is restricted to the lower latitudes of Indo-Pacific Ocean, whereas H. coerulea occurs broadly across the Indo-Pacific. Our findings highlight the effectiveness of integrating phylogenomics and morphology to resolve coral systematics, uncover cryptic species diversity, and provide new insights into speciation, diversification, and conservation of corals, thus providing a critical taxonomic basis for informing future conservation strategies for coral reef ecosystems.