DNA methylation is an essential epigenetic mark that is involved in a range of biological activities in all domains of life. Molecular mechanisms underlying how the DNA methyltransferases (DNMTs) catalyze cytosine methylation have been well documented in model species. However, it still remains underinvestigated as to how the functional divergence of different DNMT duplicates has evolved among closely related species. Here, our study addressed evolutionary dynamic, transcriptional regulation and enzyme activities of all three DNMTs (DNMT1, DNMT2, and DNMT3) in extant Poaceae species. Our results show that, although all Poaceae species are derived from the most recent common ancestor, biased genetic fractionation acting on different DNMT duplicates has resulted in high copy number variations among extant species. In addition, expression-level subfunctionalization (i.e., differential expression genes) is a common mechanism that regulates the transcriptional pattern of different DNMT duplicates in extant Poaceae species. Neo-functionalization and positive selection further promote functional divergence (i.e., different catalytic efficiency) among different DNMT duplicates. In particular, estimates of enzyme activities demonstrate that highly expressed gene copies of the DNMT1 (i.e., MET1a and MET1b) tend to show high catalytic efficiency. Furthermore, functional analyses of seven DNMT mutants also reveal that loss of function of three DNMT genes (OsCMT3a, OsCMT2, and OsDRM2) exerts complementary impacts on the transcriptional landscape. Our study provides evidence that, while DNA methylation of all three cytosine contexts (CG, CHG, and CHH) is catalyzed by the three DNMTs, different mechanisms have together promoted high evolutionary dynamic and functional divergence in extant Poaceae species.

Selligueoid ferns are arguably one of the only relatively large groups of ferns with uncertain phylogeny, biogeography, and systematics. Previous studies identified some well-supported or moderately supported clades but their relationships were largely unresolved, and thus, it remains controversial whether these ferns originated from tropical Asia or the Himalaya and how many genera should be recognized. Here, we reconstructed phylogenies based on Sanger sequencing data of five plastid markers of 261 accessions representing ca. 103 species and 67 (49 ingroup) plastomes representing 41 species of selligueoids and 18 species of outgroups. Our data resolved selligueoids into six major clades and recovered the monophyly of Arthromeris, Pichisermollodes, and Phymatopteris (excl. type) + Gymnogrammitis, whereas Selliguea will become monophyletic if two isolated species are excluded. Contrasting lumping all genera into one genus, here, we propose to recognize six genera: Arthromeris, Phymatopteris, Pichisermollodes, Selliguea, Coumariphylla (four spp.), and Vietiglossa (one sp.), in addition to the hybrid genus, × Phymatomeris. We support the proposal to conserve Phymatopteris with a new type. Phymatopteris and Selliguea are found not to co-occur in any locality. Our results suggested that selligueoids originated in the late Eocene (ca. 36.4 Mya) in the Malesia-Pacific area, consistent with the tropical Asian origin hypothesis. Quite surprisingly, only two long-distance dispersals and local range expansions/diversifications contributed to the current distribution pattern of selligueoid ferns. In support of our classification, we provide a key to the six genera, their morphological and geographical synopses, and lists of their constituent species and important synonyms.

Orchidantha, the sole genus in the family Lowiaceae (Zingiberales), shows distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite their ecological and ornamental value, many Orchidantha species are endangered and face an elevated risk of extinction. Here, we present the first chromosome-scale genome assembly of the endangered Orchidantha insularis from Hainan Island. The 2.24 Gb genome was assembled into nine pseudochromosomes, and 31 541 protein-coding genes were annotated. Phylogenomic analysis places O. insularis within the “banana group” of Zingiberales and indicates divergence from Musaceae approximately 65 Ma, following a shared recent whole-genome duplication (WGD). We identify significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to low-light tropical understory habitats. Our analysis uncovers the genetic basis of the carrion-like floral scent in O. insularis by revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole. In parallel, the expansions of flavin-containing monooxygenase (FMO) genes and signatures of positive selection reinforce indole metabolism, which links floral scent production to both adaptation and defense. Whole-genome resequencing of population samples revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks, followed by continued population decline. Together, these results provide a genomic foundation for understanding genome evolution in early-diverging Zingiberales and inform conservation and horticultural use.

Singing is a key innovation that drives the diversification of crickets. However, acoustic-related traits have not been investigated in a broad phylogenetic context, making the evolution of acoustic communication enigmatic. To explore the evolution and regression of singing and hearing, we examined over 100 species of tree crickets (Oecanthidae), a family with diverse acoustic-related traits that has never been considered in an evolutionary context. We investigated homologous traits related to sound production (stridulatory file, harp, and mirror) and reception (tympana, inner, and outer). Using a robust, time-calibrated molecular phylogeny, we estimated ancestral states and evolutionary rates and tested for correlated evolution. We quantified the phylogenetic signal for each trait to assess how evolutionary relatedness predicted acoustic trait similarity. Our analyses revealed multiple independent losses of sound-producing structures in the forewings and hearing organs, providing evidence for the convergent evolution of the silent phenotype. Our results also suggest a high level of integration among wing veins, particularly those related to acoustic communication. We discuss the potential ecological drivers of these patterns, such as predator avoidance and habitat shifts, and substantiate how alternative phenotypes, like “silent listeners” and “deaf singers”, facilitate evolutionary transitions between acoustic and vibratory signaling (biotremology). Our findings provide a model for understanding the macroevolutionary dynamics of sensory regression, a pattern shared across diverse animal systems. The evolutionary trends in the acoustic signaling of Oecanthidae provide a powerful system for studying the macroevolutionary dynamics of communication.

Sex chromosomes frequently undergo turnover through the recruitment of new sex-determining genes or translocation of ancestral genes. This phenomenon is particularly evident in Salix (Salicaceae). In Populus, the sister genus of Salix, a partial-ARR17-based sex-determination mechanism has been reported, and is also found in several Salix species. In Vetrix 15ZW clade I of Salix, species share a female heterogamety system on chromosome 15. A partial-PI (PISTILLATA)-based mechanism has been proposed for several species in this clade, except for Salix purpurea, which appears to use a two-gene model involving ARR17 and GATA15. To further investigate the evolution of sex-determining factors in this clade, we assembled a high-quality, haplotype-resolved genome of Salix integra, a close relative of S. purpurea. Based on resequencing data from males and females, we identified W and Z-linked regions located in pericentromeric regions on chromosome 15, consistent with those reported in other Salix species. Comparative analyses showed that S. integra possesses a partial-PI-based mechanism, supporting the hypothesis that PI sequences were recruited in the ancestor of 15ZW clade I, whereas the ancestor of S. purpurea recruited a two-gene model later. Together, these results advance our understanding of the relationship between sex-determining plasticity and sex chromosome evolution in plants.

The Eurasian and North African Asparagaceae subtribe Hyacinthinae Parl. comprises 15–21 genera of mostly spring‐flowering bulbs with great diversity in the Mediterranean. Many genera are horticulturally important, notably hyacinths, grape hyacinths, and squills. Understanding of relationships among these genera remains limited, with widely differing classifications in use and scattered phylogenetic sampling. A comprehensive morphological investigation of the Hyacinthinae increased the number of recognized genera from nine to 21, based largely on bulb characteristics. However, this treatment has not been widely adopted despite some support from later molecular analyses. This case study on the generic limits of a horticulturally important plant group raises key issues of gaining user acceptance of a nomenclatural system where some familiar genera are substantially redefined. To date, there has not been a detailed combined molecular and morphological study of the subtribe. We reconstructed the most comprehensively sampled phylogeny of Hyacinthinae to date, using 246 low‐copy nuclear genes from Angiosperms353 and plastome sequences. Morphological data were compiled from published literature and direct observations. Our nuclear and plastid phylogenies of Hyacinthinae recover 18 of 21 possible genera, while the remaining three are para‐ or polyphyletic. However, relationships among the genera vary between data sets. Quartet scores indicate incomplete lineage sorting or hybridization/introgression, especially where there is cytonuclear discordance. Our data provide strong support for the transfer of two species of Hyacinthus to Fessia, illustrating the problems arising from convergent floral traits. This paper offers a major step forward in the delimitation of Hyacinthinae genera.

Nymphaeales, an early-diverging angiosperm order, is pivotal for understanding floral evolution; yet, the processes of floral organogenesis and the evolutionary transitions between Cabombaceae and Nymphaeaceae remain incompletely resolved. Here, we integrate scanning electron microscopy, phylogeny-based ancestral state reconstruction, and comparative genomics to investigate floral organogenesis and MADS-box gene families in Brasenia schreberi (Cabombaceae) and Euryale ferox (Nymphaeaceae). Brasenia schreberi shows a stable trimerous, whorled initiation pattern; its floral apex remains dome-shaped and produces a superior gynoecium with free (apocarpous) carpels. In contrast, E. ferox displays a tetramerous pattern with unidirectional (abaxial-to-adaxial) initiation, followed by spiral centripetal organ formation; its apex becomes concave early, forming a complex receptacle that develops into an inferior gynoecium with syncarpous carpels. Ancestral state reconstructions indicate that Cabombaceae retains more plesiomorphic traits of the Nymphaeales ancestor, whereas Nymphaeaceae shows multiple derived innovations. Using a domain- validated, de-redundant data set, we further compare MADS-box phylogeny and motif architectures, revealing relatively conserved motifs in ABCDE-related MIKC clades but more heterogeneous patterns in certain non-ABCDE lineages, partly influenced by annotation quality. Together, these results support independent evolutionary trajectories for Cabombaceae and Nymphaeaceae and shed light on the evolution of floral organization in basal angiosperms.

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 taxonomic 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 were 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 illustrates how dispersal, climatic change, and lineage-specific diversification have interacted to generate pantropical biodiversity.

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 39 recognized 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, 10 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 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 phylum Acidobacteriota is both extraordinarily widespread and abundant, playing 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 show 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 cluster 7, derived from various environments, are strictly anaerobic, relying on nitrate/nitrite reduction or fermentation; also, cluster 5 has a limited carbon utilization range. Our analyses have also identified previously unrecognized roles in C1 metabolic pathways, the Calvin cycle, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification among the uncultured Acidobacteriota, indicating that Acidobacteriota represent overlooked important functions 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.

Crataegus L. (hawthorns) is a taxonomically challenging genus within the Rosaceae family, showing 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, Crataegus subg. Crataegus and Crataegus 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.

Conifers 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 aspects 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 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 1035 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 shows 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 (i) support Fu′s taxonomic treatment of O. sect. Schoenlandia as the independent genus Kungia; (ii) do not support merging O. subsect. Orostachys (=the O. malacophylla clade) with Hylotelephium; and (iii) suggest that O. subsect. Orostachys should be taxonomically recognized as a new genus Amblystachys and make the relevant new combinations.

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.

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 the species-level phylogeny of Euphorbieae and elucidating the biogeographic drivers of its global distribution. Among the total of 34 sampled species in Euphoroideae, 28 species were applied to represent all five genera in three subtribes of Euphorbieae, including 10 newly sequenced species representing 10 of the 11 extant species of Anthosteminae and Neoguillauminiinae, plus 18 representative Euphorbia (Euphorbiinae) species. Using plastome and nuclear ribosomal DNA (nrDNA) data sets, we reconstructed phylogenetic relationships, estimated the divergence times 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 toward understanding the role of key innovations and climatic shifts in plant diversification.

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 a blue skeleton, a 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 of China, 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.

The distribution patterns of plants in the Northern Hemisphere are closely linked to their evolutionary history. The genus Lonicera, commonly referred to as honeysuckle, is widely distributed across the northern temperate zone, making it an ideal model for exploring the distribution patterns and driving factors of plants in the Northern Hemisphere. This study, based on 108 globally distributed Lonicera samples (57 species), covered 22 of the 25 subsections of Lonicera recognized by Rehder (1903) and Nakai (1938), analyzed 485 orthologous loci and plastid genomes to investigate phylogenetic relationships, and observed phylogenetic incongruence. QuIBL and f-branch analyses revealed that incomplete lineage sorting (ILS) is the primary driver of phylogenetic discordance, accompanied by widespread but weak introgression, with only a small proportion of triplets showing strong support for introgression with relatively high mixture weights. Biogeographic and diversity distribution analyses suggest that Lonicera originated in the Qinghai–Xizang Plateau (QXP) and/or East Asia, spread to North America and Europe, and established diversity centers in East Asia, Central Europe, and western North America. Our results support the hypothesis that the uplift of the QXP and global climate shift of the Eocene–Oligocene transition (EOT) were both evolutionary drivers, with varied ecological adaptability among various Lonicera lineages. This study provides new insights into the phylogeny and biogeographic evolution of Lonicera, while also serving as a reference for studies on the evolutionary history of plant and animal lineages.

Understanding the genetic basis of phenotypic diversity is fundamental to evolutionary biology and selective breeding. The White Cloud Mountain minnow (Tanichthys albonubes) is a renowned ornamental fish, yet the genomic basis of its prized ornamental traits (e.g., golden body color and long-fin) remains poorly understood. Here, we present a high-quality chromosome-level genome assembly for T. albonubes, which has a size of 1067.12 Mb with contig and scaffold N50 values of 5.65 Mb and 41.71 Mb, respectively. A total of 1036.50 Mb (97.13%) was anchored into 25 pseudo-chromosomes. The genome is highly repetitive (53.48% repetitive sequences) and encodes 24 121 protein-coding genes. Based on this reference genome and whole genome resequencing data of 126 individuals from four populations (one wild population, one native hatchery population, golden strain and long-fin strain), we revealed that the golden strain originated directly from the native hatchery stock, while the long-fin strain was derived from a distinct wild lineage. By integrating window-based pairwise F_ST scans with GWAS analysis, we demonstrated that the golden body color is a monogenic trait, with chrna2b on chromosome 15 as a prime candidate. In contrast, we found fin elongation is a polygenic trait and identified four candidate genes (mosmob, tbx18, vwa8, wnt6b) and the hedgehog signaling pathway underpinned this long-fin phenotype. Our study provides fundamental genomic resources and unveils the genetic architecture underlying two striking ornamental traits of T. albonubes, offering crucial insights for its further selective breeding and conservation.

The tribe Trichosporeae is the most species-rich, systemically complex, and morphologically diverse tribe in the Old World Gesneriaceae. It has long been a focal point and a challenge in the phylogeny of Trichosporeae, with frequent unclear relationships and delimitations among a lot of genera. Here, we conducted a molecular phylogenetic analysis by employing nine DNA fragments with a high sampling coverage for key clades in the tribe Trichosporeae. Meanwhile, we carried out a comprehensive morphological and anatomical investigation on vegetative and floral organs in related genera and species, and try to uncover morphological synapomorphies associated with molecular clades. Our results demonstrated a well-supported phylogeny of major clades in the tribe, strongly corroborated by morphological data. We find that some genera, such as Raphiocarpus, Briggsia, and Boeica, are not monophyletic. Based on molecular phylogenetic and morphological analyses, we established five new genera and revived a genus in the tribe Trichosporeae, including Neoraphiocarpus, Anisophyllaea, Hispidopalata, Pseudobriggsia, and Kaiyua with revival of Boeicopsis. We further redefined the genera Raphiocarpus and Briggsiopsis. Our results would deepen our understanding about the phylogeny of the Old World Gesneriaceae.