Journal of Systematics and Evolution

Abstract Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

Abstract Based on recent molecular and morphological studies we present a modern worldwide phylogenetic classification of the ± 12074 grasses and place the 771 grass genera into 12 subfamilies (Anomochlooideae, Aristidoideae, Arundinoideae, Bambusoideae, Chloridoideae, Danthonioideae, Micraioideae, Oryzoideae, Panicoideae, Pharoideae, Puelioideae, and Pooideae), 6 supertribes (Andropogonodae, Arundinarodae, Bambusodae, Panicodae, Poodae, Triticodae), 51 tribes (Ampelodesmeae, Andropogoneae, Anomochloeae, Aristideae, Arundinarieae, Arundineae, Arundinelleae, Atractocarpeae, Bambuseae, Brachyelytreae, Brachypodieae, Bromeae, Brylkinieae, Centotheceae, Centropodieae, Chasmanthieae, Cynodonteae, Cyperochloeae, Danthonieae, Diarrheneae, Ehrharteae, Eragrostideae, Eriachneae, Guaduellieae, Gynerieae, Hubbardieae, Isachneae, Littledaleeae, Lygeeae, Meliceae, Micraireae, Molinieae, Nardeae, Olyreae, Oryzeae, Paniceae, Paspaleae, Phaenospermateae, Phareae, Phyllorachideae, Poeae, Steyermarkochloeae, Stipeae, Streptochaeteae, Streptogyneae, Thysanolaeneae, Triraphideae, Tristachyideae, Triticeae, Zeugiteae, and Zoysieae), and 80 subtribes (Aeluropodinae, Agrostidinae, Airinae, Ammochloinae, Andropogoninae, Anthephorinae, Anthistiriinae, Anthoxanthinae, Arthraxoninae, Arthropogoninae, Arthrostylidiinae, Arundinariinae, Aveninae, Bambusinae, Boivinellinae, Boutelouinae, Brizinae, Buergersiochloinae, Calothecinae, Cenchrinae, Chionachninae, Chusqueinae, Coicinae, Coleanthinae, Cotteinae, Cteniinae, Cynosurinae, Dactylidinae, Dichantheliinae, Dimeriinae, Duthieinae, Eleusininae, Eragrostidinae, Farragininae, Germainiinae, Gouiniinae, Guaduinae, Gymnopogoninae, Hickeliinae, Hilariinae, Holcinae, Hordeinae, Ischaeminae, Loliinae, Melinidinae, Melocanninae, Miliinae, Monanthochloinae, Muhlenbergiinae, Neurachninae, Olyrinae, Orcuttiinae, Oryzinae, Otachyriinae, Panicinae, Pappophorinae, Parapholiinae, Parianinae, Paspalinae, Perotidinae, Phalaridinae, Poinae, Racemobambosinae, Rottboelliinae, Saccharinae, Scleropogoninae, Scolochloinae, Sesleriinae, Sorghinae, Sporobolinae, Torreyochloinae, Traginae, Trichoneurinae, Triodiinae, Tripogoninae, Tripsacinae, Triticinae, Unioliinae, Zizaniinae, and Zoysiinae). In addition, we include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. We use the subfamilial name, Oryzoideae, over Ehrhartoideae because the latter was initially published as a misplaced rank, and we circumscribe Molinieae to include 13 Arundinoideae genera. The subtribe Calothecinae is newly described and the tribe Littledaleeae is new at that rank.

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge- netic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incor- rect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applica- tions of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computa- tional power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.

Abstract We present a new worldwide phylogenetic classification of 11 506 grass species in 768 genera, 12 subfamilies, seven supertribes, 52 tribes, five supersubtribes, and 90 subtribes; and compare two phylogenetic classifications of the grass family published in 2015 (Soreng et al. and Kellogg). The subfamilies (in descending order based on the number of species) are Pooideae with 3968 species in 202 genera, 15 tribes, and 30 subtribes; Panicoideae with 3241 species in 247 genera, 13 tribes, and 19 subtribes; Bambusoideae with 1670 species in 125 genera, three tribes, and 15 subtribes; Chloridoideae with 1602 species in 124 genera, five tribes, and 26 subtribes; Aristidoideae with 367 species in three genera, and one tribe; Danthonioideae with 292 species in 19 genera, and one tribe; Micrairoideae with 184 species in eight genera, and three tribes; Oryzoideae with 115 species in 19 genera, four tribes, and two subtribes; Arundinoideae with 40 species in 14 genera, two tribes, and two subtribes; Pharoideae with 12 species in three genera, and one tribe; Puelioideae with 11 species in two genera, and two tribes; and the Anomochlooideae with four species in two genera, and two tribes. We also include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. Newly described taxa include: supertribes Melicodae and Nardodae; supersubtribes Agrostidodinae, Boutelouodinae, Gouiniodinae, Loliodinae, and Poodinae; and subtribes Echinopogoninae and Ventenatinae.

Abstract Molecular phylogenetic studies have become a major area of interest in plant systematics, and their impacts on historical biogeographic hypotheses are not to be disregarded. In Brazil, most historical biogeographic studies have relied on animal phylogenies, whereas plant biogeographic studies have largely lacked a phylogenetic component, having a limited utility for historical biogeography. That country, however, is of great importance for most biogeographic studies of lowland tropical South America, and it includes areas from a number of biogeographic regions of the continent. Important biogeographic reports have been published as part of phylogenetic studies, taxonomic monographs, and regional accounts for small areas or phytogeographic domains, but the available information is subsequently scattered and sometimes hard to find. In this paper we review some relevant angiosperm biogeographic studies in Brazil. Initially we briefly discuss the importance of other continents as source areas for the South American flora. Then we present a subdivision of Brazil into phytogeographic domains, and we cite studies that have explored the detection of biogeographic units (areas of endemism) and how they are historically related among those domains. Examples of plant taxa that could be used to test some biogeographic hypotheses are provided throughout, as well as taxa that exemplify several patterns of endemism and disjunction in the Brazilian angiosperm flora.

Abstract We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably known from the fossil record. Most of these are woody (with two exceptions), and most are today either broadly East Asian, or more specifically confined to Sino‐Japanese subcategory rather than being endemic to the Sino‐Himalayan area. Of the “eastern Asian endemic” genera so far known from the fossil record, the majority formerly occurred in Europe and/or North America, indicating that eastern Asia served as a late Tertiary or Quaternary refugium for taxa. Hence, many of these genera may have originated in other parts of the Northern Hemisphere and expanded their ranges across continents and former sea barriers when tectonic and climatic conditions allowed, leading to their arrival in eastern Asia. Although clear evidence for paleoendemism is provided by the gymnosperms Amentotaxus, Cathaya, Cephalotaxus, Cunninghamia, Cryptomeria, Glyptostrobus, Ginkgo, Keteleeria, Metasequoia, Nothotsuga, Pseudolarix, Sciadopitys , and Taiwania , and the angiosperms Cercidiphyllum, Choerospondias, Corylopsis, Craigia, Cyclocarya, Davidia, Dipelta, Decaisnea, Diplopanax, Dipteronia, Emmenopterys, Eucommia, Euscaphis, Hemiptelea, Hovenia, Koelreuteria, Paulownia, Phellodendron, Platycarya, Pteroceltis, Rehderodendron, Sargentodoxa, Schizophragma, Sinomenium, Tapiscia, Tetracentron, Toricellia, Trapella , and Trochodendron , we cannot rule out the possibility that neoendemism plays an important role especially for herbaceous taxa in the present‐day flora of Asia, particularly in the Sino‐Himalayan region. In addition to reviewing paleobotanical occurrences from the literature, we document newly recognized fossil occurrences that expand the geographic and stratigraphic ranges previously known for Dipelta, Pteroceltis , and Toricellia.

Abstract DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, matK, trnH‐psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and cost‐effective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors.

Abstract Since the endosymbiont origin from α‐Proteobacteria, mitochondrial genomes have undergone extremely divergent evolutionary trajectories among eukaryotic lineages. Compared with the relatively compact and conserved animal mitochondrial genomes, plant mitochondrial genomes have many unique features, especially their large and complex genomic arrangements. The sizes of fully sequenced plant mitochondrial genomes span over a 100‐fold range from 66 kb in Viscum scurruloideum to 11 000 kb in Silene conica . In addition to the typical circular structure, some species of plants also possess linear, and even multichromosomal, architectures. In contrast with the thousands of fully sequenced animal mitochondrial genomes and plant plastid genomes, only around 200 fully sequenced land plant mitochondrial genomes have been published, with many being only draft assemblies. In this review, we summarize some of the known novel characteristics found in plant mitochondrial genomes, with special emphasis on multichromosomal structures described in recent publications. Finally, we discuss the future prospects for studying the inheritance patterns of multichromosomal plant mitochondria and examining architectural variation at different levels of taxonomic organization—including at the population level.

Abstract This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian–North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.

Abstract Phylogeography has been one major focus of evolutionary biology in recent years, with many important advances in Chinese species. In this issue, we collected 11 phylogeographic studies of plants by Chinese laboratories. We further synthesized the main findings and patterns emerging from these and previous phylogeographic studies in China and asked where phylogeographic research should be directed in the coming years. Numerous examples have shown that phylogeographic patterns in China did not show an expected expansion–contraction pattern at large scale, mirroring the geological records showing that no unified ice sheet had developed in China during the Quaternary Period. Instead, regional expansions and intraspecific divergences are very common in most studied species during the Quaternary oscillations. Different intraspecific lineages or alleles (haplotypes) were detected in multiple localized refugia, from where regional or local expansions are likely to have started. Hybridizations and introgressions are frequent between intraspecific lineages or between different species. We also reviewed computational methods for phylogeographic analyses. Despite the great progress made in recent years, there remains much to discover about the spatial–temporal dimensions and underlying speciation mechanisms of Chinese plants. Phylogeographic studies represent a key knot that connects the genus phylogeny (macroevolution) and speciation and adaptation (microevolution). Therefore, we advocate that: (i) phylogeographic studies of plants in China should be directed to the closely related species or a monophyletic group (for example, a genus or a section) in the coming years; and (ii) population genetic data based on direct sequencing multiple loci, especially those from nuclear genome and statistical tests should be widely adopted and enforced. The recovered intraspecific divergences and phylogeographic patterns of multiple‐species may allow us to better understand the high plant diversity in China and set up concrete hypotheses for studying plant speciation and diversification mechanisms in this region.

Abstract The class Thermoleophilia represents a deep‐branching lineage within the phylum Actinomycetota , and yet, its taxonomic diversity remains incompletely resolved due to the limited availability of cultured representatives and uneven integration of genome‐resolved diversity. Here, we performed an integrative phylogenomic and taxonomic analysis of Thermoleophilia using three newly generated genomes derived from desert soils in Xinjiang, China, including two cultured isolate genomes and one metagenome‐assembled genome (MAG), together with publicly available MAGs. Phylogenomic reconstruction based on conserved marker genes, overall genome relatedness indices (OGRIs), and 16S rRNA gene sequences revealed several well‐supported lineages that expand the currently characterized diversity within the order Solirubrobacterales . Strain SYSU D00693 T represents a novel family, genus, and species, for which the names Vescideserticolaceae fam. nov., Vescideserticola gen. nov., and Vescideserticola fastidiosus sp. nov. are proposed. Strain SYSU D01012 T represents a novel species within the genus Patulibacter , designated Patulibacter desertihabitans sp. nov. Genome‐based analyses further demonstrated that BS_bin.015, together with BP_457 and BP_458, forms a distinct lineage corresponding to the GTDB placeholder genus AC‐38. Phylogenomic and comparative genomic evidence supports the proposal of Candidatus Sabulibiaceae fam. nov. and Candidatus Sabulibium gen. nov., comprising three candidate species‐level lineages. Comparative genomic analyses further revealed lineage‐associated variations in genomic functional potential among the analyzed genomes. Collectively, this study expands the currently characterized taxonomic diversity of Thermoleophilia and provides genomic insights into the diversity and evolutionary relationships of this underexplored bacterial class.

Abstract We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of the APG classification were largely based on uniparentally inherited markers (plastid DNA, typically maternally inherited), there has emerged since APG IV extensive evidence of widespread hybridization and inheritance of ancestral polymorphisms. Despite this evidence of gene‐tree discordance, most of the APG IV classification is supported by both plastid and nuclear analyses, and only a few revisions are required in this update to make the classification parallel phylogenetic results in the literature. At the ordinal level, few changes in circumscription are required relative to the last APG version, although the fabids now comprise only the four nitrogen‐fixing orders (Cucurbitales, Fabales, Fagales, and Rosales) and the malvids now include the former COM clade (Celastrales, Malpighiales, and Oxalidales), which, in nuclear DNA analyses, is no longer monophyletic. Oncothecales (with only Oncothecaceae) and Cardiopteridales (with Cardiopteridaceae and Stemonuraceae) are newly recognized, and Icacinales are restricted to Icacinaceae. Restriction of Aquifoliales and Bruniales to just Aquifoliaceae/Helwingiaceae and Bruniaceae, respectively, is also proposed. Huaceae and Columelliaceae are unplaced to order among the malvids and campanulids, respectively. At the family level, expanded circumscriptions include Tecophilaeaceae (including Ixioliriaceae, Asparagales), Frankeniaceae (including Tamaricaceae, Caryophyllales), Phytolaccaceae (including Agdestidaceae and Sarcobataceae, Caryophyllales), Helwingiaceae (including Phyllonomaceae, Aquifoliales), Gesneriaceae (including Calceolariaceae and Peltantheraceae, Lamiales), Pentaphylacaceae (including Sladeniaceae, Ericales), and Orobanchaceae (including Mazaceae, Paulowniaceae, Phrymaceae, and Wightiaceae, Lamiales). In Santalales, the limits of Santalaceae and Olacaceae are revised, and Erythropalaceae and Strombosiaceae are recognized as distinct from Olacaceae; Balanophoraceae are maintained as distinct from Santalaceae, but this is a tentative placement. Generic relationships in Dioscoreales require more analyses before a revised family classification can be proposed, so we maintain the APG IV families of this order.

Abstract Gryllidae Laicharting, 1781, the most speciose family within Grylloidea, has a rich fossil record; yet, the phylogenetic relationships among these fossil taxa remain poorly resolved. Integration of fossil and extant lineages into a systematic framework has been impeded by sexual dimorphism and the fragmentary preservation typical of compression fossils, thereby confounding homology assessment and topological stability. Here, we describe Elongatitarsus falcatus gen. & sp. nov., represented by a male and a female specimen from mid‐Cretaceous Kachin amber, which serves as a morphological bridge linking Cretaceous and extant cricket diversity. To evaluate the phylogenetic signal and homoplasy of different morphological character partitions across fossil and extant Gryllidae, we conducted maximum parsimony analyses using three distinct matrices: a comprehensive morphological matrix, a wing venation‐only matrix, and a matrix excluding venation‐only fossils. The venation‐only matrix yielded poorly resolved topologies with low nodal support; in contrast, the comprehensive morphological matrix recovered a phylogeny partially congruent with recent molecular hypotheses at the subfamilial level, and placed E. falcatus gen. & sp. nov. within Gryllinae. Our results underscore that integrative morphological data sets are essential for reliable placement of fossil taxa. This approach provides a framework for testing the reliability of isolated wings in phylogenetic inferences, offering broader implications for evaluating fragmentary fossil records in deep‐time systematics.

Abstract Genomes provide the fundamental basis for understanding biological systems. Owing to rapid advances in sequencing technologies and assembly methods, the number of sequenced genomes has increased substantially. A high‐quality genome should have high continuity, completeness, and accuracy in its assembly, along with comprehensive and precise annotations of protein‐coding genes and other functional genomic elements. However, it is still difficult to fully achieve these standards due to technical limitations and the inherent genome complexity, especially for plant genomes. This review summarizes current major sequencing technologies and strategies for genome assembly and annotation, elucidates the major challenges encountered in the pursuit of truly high‐quality genomes, and provides practical strategies for meeting high‐quality genome standards. Finally, we highlight several emerging opportunities and promising research directions across the genomic landscape.

Abstract Opilioacarida are among the most primitive and enigmatic lineages of mites, retaining numerous plesiomorphic characters critical to understanding the early evolution of Parasitiformes. Here, we describe a new extinct family, Plesioacaridae fam. nov., from mid‐Cretaceous Kachin amber, representing the second known family within Opilioacarida. The fossil specimen, here named Plesioacarus minutus gen. et sp. nov., was investigated using high‐resolution confocal laser scanning microscopy, which revealed an exceptional suite of morphological features that clearly distinguish it from the extant family Opilioacaridae. These include dendritic prodorsal setae, a strongly U ‐shaped prodorsal furrow, a fused sternapophysis, a pair of setae posterior to the genital plate, a three‐clawed palpal apotele, and a three‐segmented tarsus I. The morphology of the palp apotele and tarsus I provides new insights into the evolution of appendage segmentation and specialization in early mites. To evaluate its systematic position, we conducted the morphological phylogenetic analysis for Opilioacarida based on 36 discrete characters scored across 22 extinct and extant taxa. The analyses consistently recovered Plesioacaridae as the sister group to all other opilioacarids. This discovery expands the known diversity of Mesozoic Opilioacarida and contributes important evidence for reconstructing the ancestral morphological groundplan and early evolutionary history of Parasitiformes.

Abstract Bulbostylis is the second‐most species‐rich genus in Abildgaardieae, comprising c. 221 species with a pantropical to warm‐temperate distribution and a remarkable ecological and morphological diversity. Despite advances in molecular phylogenetics confirming its monophyly, relationships within Bulbostylis remain poorly resolved, and previous attempts at creating infrageneric classifications are either geographically restricted or unsupported by phylogenetic evidence. Previous molecular studies have sampled fewer than 20% of the species of the genus, limiting our understanding of its evolutionary history. Here, we investigate relationships among 149 species and 3 subspecies of Bulbostylis , representing 69% of global diversity, using a universal probe kit for targeted genomic sequencing of flowering plants (Angiosperms353 probe kit). Our sampling also includes the genus Nelmesia , which we found to fall within Bulbostylis . We propose a new infrageneric classification and suggest a set of diagnostic morphological characters. Our revised infrageneric classification for Bulbostylis includes 18 sections and 8 subsections, providing a foundation for future taxonomic and evolutionary studies of this ecologically important genus.

Abstract Endosymbionts are prevalent in insects, establishing close associations with their hosts that range from mutualism to parasitism. Endosymbionts provide hosts with essential nutrients, enhance immunity, and regulate reproduction, thereby profoundly influencing host fitness and adaptive evolution. Such impacts can drive genetic divergence and even speciation over time. Consequently, endosymbionts are critical to understanding the formation of cryptic insect species, which are morphologically indistinguishable yet genetically distinct. Elucidating the mechanisms underlying cryptic speciation remains a central challenge in evolutionary biology, with endosymbionts increasingly recognized as key drivers in this process. In this review, we summarize the fundamental characteristics of insect endosymbionts and their multifaceted roles in host biology. We conceptualize endosymbionts as a critical evolutionary force, focusing on the mechanisms by which they drive cryptic speciation, including ecological adaptation divergence, genetic integration, and reproductive manipulation. By integrating current evidence and elucidating underlying mechanisms, this review presents a framework for understanding endosymbiont‐mediated cryptic speciation in insects. Research in this field holds great promise for revealing fundamental evolutionary processes and informing novel strategies for biodiversity conservation and pest management.

Abstract A new genus and species of Marsdenieae, Xua hongheensis , native to the Red River basin of Yunnan Province, China, is described here for the first time and compared with its close relatives. The plant is a perennial, pubescent, twining herb, and is characterized by having small (ca. 1 cm diam.) flowers and fleshy, erect staminal corona lobes with concave apices, and is endemic to the dry‐hot valleys of Yimen, Xinping, and Yuanjiang Counties, between 1000 and 1200 m, in Yunnan Province, China. In this study, we used plastome data to examine the tribal position of Xua within the family, and seven plastid and nuclear loci to further clarify its phylogenetic relationship. Our family‐wide phylogenetic analysis confirms that Xua is a member of Marsdenieae. Our subsequent analyses of Marsdenieae further support that Xua is a distinct genus and probably allied to Dolichopetalum , Cionura , Campestigma , Harmandiella , and Gongronema ‐ Dischidanthus ‐ Sarcolobus . Molecular dating analysis indicates that Xua originated at about 10 Ma and Xua and the five probable allies diverged rapidly over a period shorter than 3 million years, which might be facilitated by both the orogeny and the concurrent reinforcement of the East Asian monsoon system during the early Late Miocene. For this new genus and species, a description, illustration, assessment of the conservation status, and its placement in the Marsdenieae phylogenetic tree are provided.

Abstract Canavalia gladiata (Jacq.) DC. is a leguminous crop notable for its high protein content and oil rich in unsaturated fatty acids, positioning it as a valuable genetic resource for the diversification and nutritional improvement of legume species. Here, we report a gap‐free telomere‐to‐telomere (T2T) genome assembly of C. gladiata and perform phylogenomic analyses to reconstruct its evolutionary history. Integrative transcriptomic and metabolomic profiling further revealed the transcriptional regulatory networks underlying the biosynthesis of key nutritional metabolites, including amino acids and lipids. These findings lay a foundation for accelerating molecular breeding for improved nutritional quality in C. gladiata . The T2T assembly and multi‐omics resources presented herein serve as valuable references for comparative genomics and the genetic improvement of legume crops.

We assembled the chromosome-level genome of the Chinese endemic Wikstroemia monnula (1.32 Gb, 18 chromosomes) and identified 61 CesA/Csl genes. These genes are mainly expanded through dispersed duplication and are largely under purifying selection. Collinearity and Ks analyses suggest a recent lineage-specific whole-genome duplication. This high-quality genome offers a valuable resource for studying fiber formation and cell wall biosynthesis.