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 genus Magnolia belongs to Magnoliaceae, an early diverging lineage of the Magnoliales, and is cultivated globally for its high ornamental and commercial values. As a large genus in the family Magnoliaceae, Magnolia species are regarded as highly valuable in phylogenetic and conservation biological studies. However, the whole genome data of Magnolia is still relatively insufficient. Here, we present a high-quality, chromosome-level genome sequence of Magnolia sinostellata (1.86 Gb) with a scaffold N50 of 85.33 Mb. The 19 M. sinostellata genome chromosomes revealed 11 main duplications representing the subgenome. Comparative genomics analysis revealed that the variance in the number of abiotic stress resistance genes among Magnoliid species are related to different environmental adaptations. Most of the genes related to MAPK signaling and stress resistance pathways in the investigated M. sinostellata species are expanded, compared to the other species. Furthermore, the comparative genomics analysis of three Magnolia assemblies, M. sinostellata, Magnolia biondii, and Magnolia sieboldii revealed that large inversions were enriched in terpenoid metabolic pathways, stress resistance and flavonoid biosynthesis, and DNA replication proteins. Using transcriptome sequencing data, we analyzed the expression levels of genes related to terpenoid biosynthesis (terpene synthase) and ICE–CBF–COR gene models related to cold tolerance in various tissues and the buds under different temperature conditions. The high-quality assembly of M. sinostellata and the ICE–CBF–COR bioinformatic analysis cascade provide valuable resources for studying the phylogeny and evolution of Magnoliaceae and angiosperms, while the candidate genes will provide foundational support for molecular breeding in Magnolia species.

Many genera were erected without phylogenetic validation in Bittacidae, a cosmopolitan family in Mecoptera, leaving their generic statuses contentious. Here, we investigated the phylogenetic relationships and reconstructed the ancestral states of chromosome numbers and key morphological characters for 26 species in three genera of Bittacidae using an integrative approach combining molecular, cytogenetic, and morphological data. The phylogenetic analyses reveal that all three genera studied are paraphyletic, but cytogenetic evidence supports the generic status of Terrobittacus Tan & Hua with haploid chromosome numbers ≥20. In contrast, the genus Bittacus Latreille, 1805 exhibits an extensive chromosomal variation from n = 8 to n = 22. Ancestral state reconstruction suggests that the diagnostic character of Bicaubittacus Tan & Hua may represent an apomorphy restricted to a few species. The cytogenetic investigation indicates that n = 22 was the ancestral chromosome number in Bittacidae. Chromosome fusions were likely responsible for numerical reduction in chromosomes of Terrobittacus, whereas more complex structural and numerical variations accounted for the chromosome diversity of Bittacus and Bicaubittacus. To satisfactorily resolve the generic problem of Bittacidae, taxon sampling should be greatly expanded at the global scale, and more attention should be paid to the integrative taxonomy.

Karst areas are well known for their extreme biodiversity and the investigation of plant adaptation in these unique environments is a research hotspot. Previous studies have primarily focused on the genomic adaptation of karst endemic species, but the specific adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas serves as a valuable model for understanding these genomic mechanisms. Here, the H. subcapitata genome was sequenced using the PacBio and Illumina platforms and de novo assembled with a contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% of sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: the γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events probably facilitate the expansion of stress-responsive gene families, which in turn influence functional pathway regulation. In particular, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared with the karst endemic Primulina tabacum, H. subcapitata showed the upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation is a unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.

The generic delimitation of the Caesalpinia group continues to be under contention, similar to several other lineages of the hyper diverse legume family. Despite its known ecological and economic importance and role as a model to explore correlations between ecological diversification and genomic traits, both intergeneric and infrageneric relationships remain unresolved, despite recent phylogenetic analyses. While phylogenomic approaches have elucidated complex relationships within the angiosperm tree of life, the phylogenetic backbone of the Caesalpinia group remains poorly defined owing to limited genomic data. To address this gap, this study combined de novo assembled and characterized plastomes from 19 samples across nine genera, along with 27 previously published plastomes, to achieve a comprehensive dataset of 46 plastomes representing 16 of the 26 genera. The phylogenomic analysis generated a robust phylogenetic hypothesis, distinguishing two main clades, of which one occurs exclusively in the Neotropics in contrast to the other Pantropical clade, in addition to resolving several previously ambiguous relationships. Notable changes in the plastome gene content were observed, including six gene losses (psbL, rpl22, rps2, rpl32, ycf1, ycf2) and six gene duplications (ndhB, rpl23, rps7, rps12, ycf1, ycf2). Other changes included shifts in inverted repeat (IR) boundaries and genome rearrangements, indicating lineage-specific plastome evolution. Hypervariable regions were identified as potential mini-barcodes, with cpSSRs providing valuable resources for species delimitation and population genetics studies. Codon usage revealed a strong AT bias, while relaxed purifying selection in genes such as accD, clpP, and rps16. These findings offer novel insights into Caesalpinia group evolution, emphasizing the utility of plastome data for resolving complex evolutionary questions and establishing a genomic toolkit for future research in systematics, conservation, and evolutionary biology of legumes.

The genus Micromonospora, a globally distributed actinomycete inhabiting diverse ecosystems, is widely recognized for its remarkable biosynthetic capacity and role as a prolific source of bioactive natural products. However, the members of the genus Micromonospora from extreme environments remain largely unstudied. In this study, we isolated 15 Micromonospora spp. strains from samples collected in desert and marine habitats. Based on polyphasic taxonomy approaches eight strains were identified and represent four novel species. Genome mining of the newly isolated strains revealed substantial biosynthetic potential for terpenes (n = 70, 22.9% of total biosynthetic gene clusters [BGCs]) and polyketides (n = 60, 19.6% of total BGCs). Subsequent pan-genomic analysis identified substantial numbers of terpene-related (n = 745, 33.8% of total biosynthetic genes [BGs]) and polyketide-related (n = 728, 33.0%) BGs in the core genome, highlighting their core biosynthetic potential. To further investigate their metabolic capacity, fermentation and metabolomic profiling were conducted to assess the secondary metabolite production capacity of all 15 strains. The results revealed a diverse array of alkaloids (averaging 75.3, 33.4% of total annotated secondary metabolites) and amino acid-derived peptides (averaging 56.3, 25.0% of total). These findings also highlight significant metabolic variations among strains and underscore the pivotal role of fermentation conditions in shaping their metabolic profiles. This study advances the taxonomic and functional understanding of Micromonospora spp. and presents a multi-omics framework combining genome mining and metabolomics to explore the biosynthetic potential of wild-type strains from extreme habitats.

Due to the high cost of whole-genome sequencing and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum, in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The EA lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.

The family Primulaceae s.l. is estimated to comprise approximately 60 genera and 2600 species worldwide. Although extensive research has been conducted on the family Primulaceae and its subfamily boundaries, there is a lack of systematic studies utilizing complete plastid genome data, leading to uncertainties in the phylogenetic positions of certain key taxa, such as Stimpsonia. In this study, plastid genomic data were collected from 67 accessions representing four subfamilies and 28 genera within the Primulaceae family. Phylogenetic trees were constructed using coalescent and concatenated approaches to elucidate the evolutionary history of the family. By employing a comprehensive dataset of 67 plastid genomes from all four subfamilies, a robust phylogenetic framework for the family was established. Contentious relationships were identified at the early stages of divergence in Primula and among Cyclamen and its relatives, probably due to rapid diversification. Our plastid genomic data support the idea that Stimpsonia is sister to the remainder of the subfamily Primuloideae, in contrast with its placement in Myrsinoideae based on nuclear data. A cytonuclear discordance in the phylogenetic position was also detected in Aegiceras corniculatum. The divergence time estimates from this study align with previous findings, indicating significant diversification events during the Eocene and Oligocene epochs. These timeframes coincide with major geological and climatic changes, which were likely to have influenced the distribution and diversification of Primulaceae. These results underscore the complex evolutionary history of the Primulaceae family and lay the groundwork for future research aimed at unraveling the intricate evolutionary dynamics within this family.

Continent-wide disjunctions, where related taxa are distributed across isolated regions within the continent, are rare in grasses and remain poorly understood. The genus Trichoneura occurs in both the New World and the Old World, with no species occurring in both continents, and its distribution displays continental disjunctions. The current distribution of African Trichoneura is said to be a result of the formation of an African arid corridor, yet this remains understudied. Using complete chloroplast genomes and nuclear genes of seven newly sequenced Trichoneura species, we studied their phylogenetic relationships and divergence history, reconstructed their ancestral history, and modeled their ecological niche to understand their evolution and current distribution pattern. Our findings revealed that the plastomes of Trichoneura are generally conserved and range in length between 135 069 and 134 139 bp. Molecular results show that Trichoneura is monophyletic and diverged around 5.78 Ma. The Late Miocene origin of this genus correlates with the formation of the African arid corridor, which explains their fragmented distribution in Africa. Dispersal and vicariance are likely to have played pivotal roles in driving their divergence, leading to subsequent distribution toward Neotropical regions during the Pliocene period. Trichoneura mollis and Trichoneura lindleyana occurring in different regions displayed varying morphology, and we suggest further morphological and phylogenetic analysis to determine their taxonomic delimitation.

When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species in East Asia and three in the Mediterranean region. Here we used target-capture sequencing and obtained 1991 single-copy nuclear genes, plus complete plastomes, to infer the evolutionary history of Cupressus. Our phylogenomic reconstruction resolved four well supported clades in Cupressus, but revealed significant phylogenetic conflicts, with inter-lineage gene flow, incomplete lineage sorting and gene tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between the ancestors of the Himalayan–Hengduan Mountains and subtropical Asia clades, whereas orogenic and climatic changes may have facilitated gene flow within the Himalayan–Hengduan Mountains clade. Molecular dating suggested that the most recent common ancestor of Cupressus appeared in East Asia around the middle Eocene period and then became continuously distributed across Eurasia. The East Asian–Tethyan disjunction arose when the Mediterranean and Himalayan–Hengduan Mountains clades diverged, likely to have been driven by Eocene/Oligocene declines in global temperature, then reinforced by the ecogeographic barrier created by the uplift of the Qinghai–Tibet Plateau. Niche shifts in the common ancestor of the Mediterranean clade, and signatures of selection in genes for drought and salt tolerance, probably indicate adaptation of this clade to local conditions. Overall, our study suggested that in-depth phylogenomic analyses are powerful tools in deciphering the complex evolutionary history of the origin of East Asian–Tethyan disjunction of organisms, especially gymnosperms.

Dennstaedtiaceae, a heterogeneous family of ferns with 11 genera and about 270 species, has a global distribution. While substantial progress has been made in elucidating the intergeneric relationships within Dennstaedtiaceae, certain nodes, particularly within Hypolepidoideae, remain controversial. To date, no phylogenomic investigation of nuclear genes has been conducted for Dennstaedtiaceae, and the biological processes underlying its complex evolution remain largely unknown. In this study, we generated transcriptome sequences from nine species in Dennstaedtiaceae and combined them with publicly available data sets from 13 species and one outgroup. By utilizing the 23 transcriptomic data sets, representing nine out of the 11 genera in Dennstaedtiaceae, we successfully resolved the intergeneric relationships within the family and established a fundamental phylogenetic framework to investigate its evolutionary history. By combining the analyses of rate-adjusted K_s-based age distributions and phylogenetic reconciliation approaches, we found evidence of at least one round of whole-genome duplication (WGD) that is shared by all Dennstaedtiaceae species prior to their divergence. Extensive gene tree discordance was found across the backbone of Dennstaedtiaceae, with the most significant discordance within Hypolepidoideae. The results of incomplete lineage sorting (ILS) simulation revealed that ILS is a substantial contributor to these conflicts. Evidence from phylogenetic networks and introgression tests indicates the occurrence of gene flow among the clades of Paesia, Hiya, and Histiopteris, potentially explaining the observed cytonuclear discordance in Hypolepidoideae. Our phylotranscriptomic study of Dennstaedtiaceae provides novel insights into its complex reticulate evolutionary history, paving the way for future studies aimed at unraveling the mechanisms underlying its diversification and adaptation.

Species are distributed heterogeneously, and different regions have contrasting numbers of species, producing species richness anomalies. More than 100 angiosperm genera demonstrate disjunct distributions in at least two of these regions: Europe, eastern North America, western North America, and East Asia, and commonly between East Asia and eastern North America. These regions have similar climates but usually exhibit species richness anomalies; however, the underlying causes of species richness anomalies in disjunct intercontinental regions remain poorly understood. In this study, we investigated the drivers of anomalies in ash tree (genus Fraxinus L.) species richness anomalies among disjunct intercontinental regions based on distribution data, macrofossil records, and corresponding evolutionary and environmental variables. Generalized linear regression and pathway model analyses incorporating environmental and evolutionary processes indicated that global cooling has contributed to low species richness in Europe, whereas evolutionary divergence, shaped the distinct species distribution patterns in East Asia (which was identified as an evolutionary cradle) and North America (which was identified as an evolutionary museum). Environmental heterogenies and evolutionary divergence have resulted in a significant diversity anomaly between these regions. This study emphasizes the important role of evolution in the formation of species richness distribution patterns.

The Asteraceae capitulum, particularly a radiate capitulum with differing colors of ray and disc florets, resembles a solitary flower probably through adaption to animal pollination. A previous study found that the shape-color association in Chrysanthemum was due to co-option of the carotenoid-cleavage-dioxygenase gene CCD4a under regulation of the ray-floret identity CYC2g, a member of floral symmetry regulators CYCLOIDEA. Then questions arise: Is such a gene co-option specific to Chrysanthemum? Or did it originate earlier in the evolution of Chrysanthemum and allies? To answer these questions, we examined 11 species representing four color patterns of radiate capitula in the tribe Anthemideae, to which Chrysanthemum belongs. Comparative examinations of carotenoid content, expression patterns of CYC2-like and CCD-like genes along floret developments, and dual-luciferase assays showed that capitular color patterns were strongly correlated with patterns of carotenoid accumulation/degeneration. In the white-ray/yellow-disc species, both CYC2g and CCD4a were ray-specifically expressed and CYC2g can activate CCD4a; in the yellow-ray/yellow-disc species, CCD4a genes were either lost or repressed by CYC2g. The white discs of Achillea alpina must be due to other regulators activating CCD4a expression. The bicolor rays of Glebionis coronaria seemed to have complex color regulation probably due to redundant function of two CCD4a paralogs. In sum, the shape-color association of a radiate capitulum is evolutionarily conserved in the tribe Anthemideae, and the underpinning gene co-option of CCD4a into the floral symmetry regulation network probably arose before divergence of the tribes Anthemideae and Astereae as the divergence of CCD4 into CCD4a and CCD4b occurred at approximately that time.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitatadapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section‐based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

Coccoidea (Hemiptera, Sternorrhyncha) are widely distributed and agriculturally significant insects known for their distinctive morphology and biological traits. The Coccoidea are often called scales or mealybugs because many species have a shell‐like covering resembling a scale or are covered with mealy wax. Knowledge of scale insects beyond the female adult stage is limited, partly because other life stages are less conspicuous, shorter‐lived, and less impactful on host plants. This complicates accurate classification, further compounded by limited molecular phylogenetic studies. This study presents the first phylogenetic analyses combining genome and transcriptome sequence data. We sequenced five whole genomes and one transcriptome from Pseudococcidae and integrated these new genome‐scale data with existing genome and transcriptome sequences to perform phylogenomic analysis of scale insects. The analysis yielded robustly supported relationships within Coccoidea, resolving several high‐level relationships. The current genome‐scale data support the monophyly of Monophlebidae, Pseudococcidae, Kerriidae, and Diaspididae, while not supporting the monophyly of Coccidae and Eriococcidae. Bayesian inferences using site‐heterogeneous models corroborated Pseudococcidae as the sister group of all other neococcoid families. Within Pseudococcidae, two subfamilies, Phenacoccinae and Pseudococcinae, were supported. At the tribe level, Phenacoccini was found to be monophyletic, whereas Planococcini, Trabutinini, and Pseudococcini were not.

Among the lineages of the tree of life, land plants exhibit a remarkably high genomic disparity because of their distinct evolutionary trajectories in the phylogenetic history of their major lineages. The macroevolutionary pattern of genomic evolution has been mainly investigated to obtain insights into well-studied lineages such as angiosperms, but little attention has been given to many important lineages such as bryophytes. This study was designed to resolve this gap by comparing the genomic evolution trajectories of mosses and liverworts. Thus, a data set comprising chromosome number and genome size was compiled, including previously published and newly generated data that were used to trace the phylogenetic history of these two parameters among mosses and liverworts via ancestral state reconstruction and phylogenetic comparative analyses. Contrasting patterns of chromosome number and genome size evolutions were detected between the two sister lineages. Mosses accumulated high chromosome number disparity via repeated whole-genome duplications and descending dysploidy but maintained a small genome size. By contrast, the chromosome number of liverworts was highly conserved, and heterogeneous trends in genome size evolution were identified among major lineages. These contrasting patterns may be partly explained by the difference in genomic dynamics: Active dynamics enables genome downsizing and reorganization in mosses, whereas genome stability leads to the accumulation of large genomes in liverworts. The results of this study confirmed the distinct trends of genomic evolution in bryophytes.

Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well-resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC, ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high-resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long-obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.

Understanding plant diversity and the phylogenetic divergences in the Northern Hemisphere is essential for in-depth evolutionary studies and conservation efforts. Maianthemum is an ideal example to explore plant diversification processes in the Northern Hemisphere, with more than 35 species widely distributed in forests in North to Central America, Europe and eastern Asia. Yet the phylogenetic relationships within Maianthemum remain elusive. In this study, we reconstructed a well-supported phylogenetic framework of Maianthemum and explored possible gene introgressions and reticulate evolution using nuclear and chloroplast genomes based on the target enrichment Hyb-Seq approach. Both nuclear and chloroplast phylogenetic results supported three clusters corresponding to their biogeographic distribution of the New World, the Himalayan-Hengduan Mountains, and the north temperate zone, respectively. The genus was inferred to be most likely originated in North America with migrations into Central America and eastern Asia in the late Miocene. Our results suggested that both incomplete lineage sorting and hybridizations/introgressions along with geographic isolation have contributed to the rapid divergence of Maianthemum in eastern Asia, which may represent a complex model for the evolutionary radiation of plants in eastern Asia and even the Northern Hemisphere.

Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population-level genomic data restriction site-associated DNA-single nucleotide polymorphisms (RAD-SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis–D. floribunda group, but with cyto-nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil-calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD-SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid-Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome-scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.

The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time-calibrated phylogeny for 749 species representing c. 80% of the genera of this clade using nrDNA ITS, plastid matK, and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil-calibrated dating analysis showed a nearly simultaneous divergence between the stem node (c. 62 Ma) and the crown node (c. 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c. 10 Ma. Possible explanations for the present-day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra- and intercontinental long-distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid-Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.

Cotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan-plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwinii–Gossypium barbadense and Gossypium hirsutum–Gossypium ekmanianum–Gossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.

The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a data set of more than 569 990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different data sets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a nonmonophyletic group, consisting of Erotyloidea, Nitiduloidea, and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early-diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.

As an important halophyte in the Yellow River Delta, the Amaranthaceae C₃ Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high-quality chromosome-scale reference genome by combining high-throughput sequencing, PacBio single molecule real-time sequencing, and Hi-C sequencing techniques with a genome size of 445.10 Mb and contigs N50 of 2.94 Mb. Through the annotation of the S. salsa genome, 298.76 Mb of the repetitive sequences and 23 965 protein-coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole-genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9 Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.

The Sui people living in Guizhou province have a unique ethnic culture and population history due to their long-time isolation from other populations. To investigate the genetic structure of Sui populations in different regions of Guizhou, we genotyped 89 individuals from four Sui populations using genome-wide single nucleotide polymorphisms arrays. We analyzed the data using principal component analysis, ADMIXTURE analysis, f-statistics, qpWave/qpAdm, TreeMix analysis, fineSTRUCTURE, and GLOBETROTTER. We found that Sui populations in Guizhou were genetically homogeneous and had a close genetic affinity with Tai-Kadai-speaking populations, Hmong-Mien-speaking Hmong, and some ancient populations from southern China. The Sui populations could be modeled as an admixture of 33.5%–37.9% of Yellow River Basin farmer-related ancestry and 62.1%–66.5% of Southeast Asian-related ancestry, indicating that the southward expansion of northern East Asian-related ancestry influenced the formation of the Tai-Kadai-speaking Sui people. Future publications of more ancient genomics in southern China could effectively provide further insight into the demographic history and population structure of the Sui people.

Rhododendron is the largest genus in Ericaceae and is well known for its diversity and beauty of flowers present in different species, making it a much-revered lineage of ornamental plants. Many species of Rhododendron are intolerant of high temperatures, which are becoming more common and intense in urban areas under global climate change. Therefore, the discovery and description of genes from heat-tolerant Rhododendron lineages are essential in the development of new climate-resilient cultivars. One such species known to be heat tolerant is Rhododendron × pulchrum Sweet. To better understand the genomics of heat tolerance in this species, we assembled a haplotype-resolved and chromosome-scale genome for R. × pulchrum, which had a genome size of 509 Mb; a scaffold N50 of 37 251 370 bp; and contained 35 610 genes. In addition, based on the same reannotation pipeline, we conducted pan-genomic analyses for all seven available chromosome-scale Rhododendron genomes and found 14 415 gene groups shared across all species and 18 018 gene groups distributed in the other species, including 1879 gene groups found in only a single species. Finally, we analyzed the transcriptomic data from heat-treated and non-heat-treated R. × pulchrum plants to quantify the genes that are most important during heat stress in an effort to inform the development of climate-resilient cultivars. This study provides insight into the genome diversity in Rhododendron and targets several genes related to agronomic traits that may help in further analysis.

Chinese Tajiks are an Indo-Iranian-speaking population in Xinjiang, northwest China. Although the complex demographic history has been characterized, the ancestral sources and genetic admixture of Indo-Iranian-speaking groups in this region remain poorly understood. We here provide the genome-wide genotyping data for over 700?000 single-nucleotide polymorphisms (SNPs) and mtDNA multiplex sequencing data in 64 Chinese male Tajik individuals from two dialect groups, Wakhi and Selekur. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, treemix, qpWave/qpAdm, Admixture-induced Linkage Disequilibrium for Evolutionary Relationships (ALDER), and Fst analyses to infer a fine-scale population genetic structure and admixture history. Our results reveal that Chinese Tajiks showed the closest affinity and similar genetic admixture pattern with ancient Xinjiang populations, especially Xinjiang samples in the historical era. Chinese Tajiks also have gene flow from European and Neolithic Iran farmers-related populations. We observed a genetic substructure in the two Tajik dialect groups. The Selekur-speaking group who lived in the county had more gene flow from East Asians than Wakhi-speaking people who inhabited the village. These results document the population movements contributed to the influx of diverse ancestries in the Xinjiang region.