Phoebe zhennan, an endemic species of Lauraceae in China, is an ecologically and economically important timber tree that has undergone severe population decline and is considered endangered. Despite its importance and threatened status, the absence of haplotype‐resolved genomic resources has hindered detailed genetic and evolutionary studies. Here, we report the first haplotype‐resolved chromosome‐level genome of P. zhennan using ONT ultra‐long reads and Hi‐C technology. The assemblies for Haplotype A (HapA, 956.20 Mb) and Haplotype B (HapB, 910.89 Mb) were each anchored to 12 chromosomes, with scaffold N50 values of 86.27 Mb and 77.12 Mb, respectively. A total of 33 757 and 33 651 protein‐coding genes were identified for HapA and HapB, respectively, of which 95% were functionally annotated. Comparative analyses revealed extensive structural heterozygosity, including 112 inversions, 2371 translocations, 6 059 780 single‐nucleotide polymorphisms (SNPs), 345 228 insertions, and 348 584 deletions. This haplotype‐resolved assembly further elucidates the characteristics of chromosomal structural variation and provides an important genetic resource for future studies on the evolution, conservation, and functional biology of P. zhennan.

Many bird species with broad geographic distributions show complex patterns of lineage divergence shaped by historical isolation, migration, and gene flow. The American robin, Turdus migratorius, is found throughout North America and includes seven described subspecies that differ in plumage and migratory behavior; yet, their evolutionary relationships remain uncertain. Here, we used genome‐wide SNP data, population structure analyses, phylogenomic inference, divergence time estimation, and D‐statistics to reconstruct relationships within the T. migratorius complex and evaluate patterns of lineage divergence and introgression. Our analyses consistently recovered four principal genomic lineages that do not correspond to currently recognized subspecies: (1) T. m. confinis from Baja California Sur, (2) a Mexican lineage, (3) western North America, and (4) boreal eastern North America. Time‐calibrated analyses indicate a deep late‐Miocene divergence (~8 Ma) separating T. m. confinis from all other lineages, followed by Pleistocene diversification among the remaining groups. Genome‐wide differentiation and long‐term isolation support the recognition of T. m. confinis as an independently evolving lineage consistent with species‐level status. In contrast, Turdus rufitorques, which is traditionally considered the sister species of T. migratorius, was nested within the Mexican lineage. Significant D‐statistics revealed excess allele sharing between the Mexican lineage and T. rufitorques, supporting a history of introgression. This study refines species limits within the American robin complex and highlights the importance of genome‐wide data for resolving evolutionary independence in widespread migratory birds.

Islands are natural laboratories for studying speciation, where geographic isolation can promote rapid diversification. This study investigates the divergence of an insular population of the orchid Epidendrum fulgens on Alcatrazes Island, a land-bridge island off the Brazilian coast. Using an integrative approach, we combined genomic (nuclear and plastid microsatellites), phenotypic (leaf functional traits and floral morphometrics), and ecological (plant community structure and diversity) analyses to test for differentiation from mainland populations. Our results revealed significant genetic divergence, with the island population exhibiting exclusive plastid haplotypes and a distinct genetic cluster, indicating prolonged reproductive isolation despite historical land connections. Phenotypically, insular plants consistently displayed succulent leaves and smaller flowers, traits suggestive of local adaptation to drier conditions and a distinct pollinator regime. Although community-level analyses revealed similar species and phylogenetic diversity, the insular community differed compositionally and exhibited a distinct phylogenetic structure. The confluence of genetic distinctness, adaptive phenotypic traits, and ecological isolation satisfies multiple species criteria, leading us to describe the Alcatrazes population as a new cryptic species. This finding underscores the role of land-bridge islands as engines of speciation, even for species with high dispersal potential, and highlights the critical importance of integrative taxonomy for identifying evolutionarily significant units and informing conservation efforts for insular endemics.

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.

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.

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.

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.

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.