The origin and speciation of orchids

Exploring the potential of Angiosperms353 markers for species identification of Eastern Mediterranean orchids

Tuberous orchids are ecologically vulnerable species, threatened by a range of environmental pressures such as overharvesting, grazing and land use change. Conservation efforts require accurate species identification, but are impeded by limited phylogenetic resolution of traditional genetic markers, which is exacerbated by widespread taxonomic conflict regarding the classification of orchids. Target enrichment holds promise to resolve both these challenges by offering a large set of nuclear loci with which to increase phylogenetic resolution and evaluate competing species models. Here, we evaluate the effectiveness of the Angiosperms353 markers for distinguishing over 50 tuberous orchid species native to Greece and we explore the possibility of narrowing these markers to a smaller set that could function as a minimal probe set. Our methodology consists of a three-tiered approach: 1) generating a species-level phylogeny using all Angiosperms353 loci with sufficient target recovery, 2) evaluating competing species models based on "splitter" and "lumper" classifications through Bayes Factor species delimitation, and 3) ranking the potential of Angiosperms353 loci to discriminate representatives of lineages with different divergence times based on their phylogenetic informativeness. While the inferred multi-species coalescent phylogeny had overall high support, Bayes Factor delimitation revealed mixed outcomes, favouring splitting in Serapias, while favouring splitting in basal clades and lumping in more recently diverged clades in Ophrys. A molecular clock analysis of Ophrys confirms rapid and recent radiation in clades marked by phylogenetic uncertainty, suggesting the need for additional loci to fully resolve this genus. Finally, we found 30 loci to be highly phylogenetically informative across four epochs of Orchidinae evolution; we suggest these are promising candidates for future marker development. Our findings enhance the Plant Tree of Life (PAFTOL) by contributing additional phylogenomic data for species that were previously underrepresented in trees built with these markers, while shedding light on the ongoing "splitter"-vs-"lumper" debate and offering new directions for species identification of tuberous orchids, a group with distinct taxonomic and conservation challenges.

Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum

Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.

Areas of endemism of semiaquatic bugs (Hemiptera: Gerromorpha): an approach to the biogeographic regionalization of Colombia

Areas of endemism, defined by the congruence of the distribution of two or more taxa that are only found in that specific area, are considered an important input for biogeographic regionalization and determining priority areas for conservation. Herein we inferred the areas of endemism of Gerromorpha and their representation within the current protected areas system of Colombia. We analyzed 480 records of 69 species of semiaquatic bugs (Hemiptera - Gerromorpha) using the NDM/VNDM and three different grid sizes. We identified eight areas of endemism and 15 endemic species belonging to the genera Altavelia, Hydrometra, Oiovelia, Microvelia, Platygerris, Potamobates, Rhagovelia, Rheumatobates, Stridulivelia, Telmatometropsis and Veloidea. We identified five consensus areas. The endemism patterns of Gerromorpha from smaller units within the biogeographic provinces proposed by Morrone (Zootaxa 2014, 3782, 1-110). Rather, they form smaller units within provinces, similar to those found in vertebrates, suggesting the existence of biogeographic districts and therefore the need for a new classification. Only six of the 15 endemic species are protected under the current protected areas system. Defining Gerromorpha AEs constitutes a first step to infer the biogeographic history and the evolutionary processes that influence the distribution of semiaquatic bugs in Colombia and guide actions for their conservation.

Orchid phylogenetics and evolution: history, current status and prospects

BACKGROUND

Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes - morphological, ecological and molecular - that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800s, which were based solely on morphology, and now is largely based on genomic analysis. The resulting patterns have been used to update family classification and to test many evolutionary hypotheses in the family.

SCOPE

Recent analyses with dense sampling and large numbers of nuclear loci have yielded well-supported trees that have confirmed many longstanding hypotheses and overturned others. They are being used to understand evolutionary change and diversification in the family. These include dating the origination of the family, analysis of change in ecological habit (from terrestrial to epiphytic and back again in some cases), revealing significant plastid genome change in leafless holomycotrophs, studying biogeographic patterns in various parts of the world, and interpreting patterns of fungal associations with orchids.

CONCLUSIONS

Understanding of orchid relationships has progressed significantly in recent decades, especially since DNA sequence data have been available. These data have contributed to an increasingly refined classification of orchids and the pattern has facilitated many studies on character evolution and diversification in the family. Whole-genome studies of the family are just beginning and promise to reveal fine-level details underlying structure and function in these plants, and, when set in a phylogenetic context, provide a much richer understanding of how the family has been so successful in diversification.

Rapid loss of plastid ndh genes in slipper orchids (Cypripedioideae, Orchidaceae)

Introduction

The eleven plastid ndh genes encode for subunits of the ndh (NAD(P)H dehydrogenase-like) complex, which mediates electron flow in photosystem I. The loss of ndh genes in plants was observed in many different lineages of Viridiplantae. In lineages of Orchidaceae, the loss of ndh genes was often associated with myco-heterotrophy. However, in previous studies on this topic only a few slipper orchids were included. Our study aimed to analyze the loss of ndh genes within Cypripedioideae, a subfamily that is assumed to be fully autotroph.

Methods

Based on a comprehensive sampling of 100 published plastomes representing 60% of Cypripedioideae species, the phylogenetic relationships were revealed on three levels. For family and subfamily levels, 57 and 66 plastid genes, respectively, were extracted and concatenated in Geneious, while for the genus-level phylogeny, complete plastomes were used to calculate a maximum likelihood tree. Additionally, divergence time estimates were performed to illuminate the evolutionary timeframe of the gene loss. The prevalence, pseudogenization and loss of ndh genes were assessed and visualized along the phylogenetic trees.

Results

The results confirmed the four analyzed genera of Cypripedioideae to be monophyletic and could increase the resolution within the genera compared to previous studies. The diversification of the subfamily started at about 30 Ma with genus Paphiopedilum displaying the most recent diversification starting at about 11 Ma and showing most speciation events around 4 Ma. The rapid loss of plastid ndh genes within the subfamily Cypripedioideae, particularly in the genera Mexipedium, Phragmipedium and Paphiopedilum could be illustrated. Furthermore, the results illustrated that Cypripedioideae are in an early stage of plastid degradation.

Discussion and conclusions

Recent studies showed that partial myco-heterotrophy (mixotrophy) is far more common in plant lineages than originally assumed. Based on our findings, we suggest that the possibility of a mixotrophic lifestyle within (sub-)tropical slipper orchids should be reevaluated. Further research regarding the reasons behind plastid gene loss in slipper orchids could provide a better understanding of the ecological evolution of Cypripedioideae.

In Situ Conservation of Orchidaceae Diversity in the Intercontinental Biosphere Reserve of the Mediterranean (Moroccan Part)

The focus of this study was the Intercontinental Biosphere Reserve of the Mediterranean (IBRM, part of the biodiversity hotspot of the Mediterranean Basin) and the Orchidaceae family, which is under-studied in the Moroccan part of the IBRM. For this reason, an inventory of Orchidaceae diversity and factors that could influence their in situ conservation was undertaken, employing a series of field surveys conducted in the Northern Moroccan IBRM ecosystems. In total, 42 sites were surveyed in four protected areas of the Moroccan part of the IBRM. In total, 21 Orchidaceae species and subspecies (taxa) belonging to seven genera were identified, including Orchis spitzelii subsp. cazorlensis, as newly recorded in Morocco, as well as several new reports for different sites and/or areas surveyed, thus updating the previous knowledge of Moroccan Orchidaceae. Most of the Orchidaceae taxa were found in limited numbers of individuals (<30) and were restricted in a few sites (1-3) or a single area; thus, they were assessed as poorly conserved due to the scarcity of rainfall coupled with human pressures, such as the abstraction of surface water, forest fires, and the conversion of protected forests to Cannabis farms. The enforcement of existing laws, the adoption of strategies to combat desertification and forest fires, the prohibition of Cannabis farming, and raising awareness among the local population could reduce the pressures on the protected Orchidaceae members and their habitats, thereby contributing to their conservation.

Persistent Habitat Instability and Patchiness, Sexual Attraction, Founder Events, Drift and Selection: A Recipe for Rapid Diversification of Orchids

Orchidaceae is one of the most species-rich families of flowering plants, with most current diversity having evolved within the last 5 My. Patterns associated with species richness and rapid diversification have been identified but have not often been associated with evolutionary processes. We review the most frequently identified correlates of diversity and suggest that the processes and rate by which they occur vary geographically and are largely dependent on persistent pulses of habitat instabilities, especially for epiphytes. Aggressive orogenesis creates fragmented habitats while global climatic cycles exacerbate the ecological instabilities. The need for repeated cycles of dispersal results in frequent founder events, which sets the stage for allopatric diversification via bouts of genetic drift and natural selection. The allopatry requirement can be bypassed by pollination systems involving flowers attracting pollinators through the production of sex signaling semiochemicals. The drift-selection model of diversification, coupled with persistent habitat instability throughout ecological and geological time scales, and sex signaling are the likely components of a multifactorial process leading to the rapid, recent diversification in this family.

Ultra-performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry-Based Profiling and Evaluation of Antioxidant, Antityrosinase, Antimicrobial and Antiproliferative Activities of Eulophia nuda Lindl.: A Medicinal Orchid

Eulophia nuda Lndl., a terrestrial medicinal orchid, is well known for its ethnomedicinal applications in treating bronchitis, tuberculosis, tumours, snake bites and arthritis. This study aimed to identify the phytoconstituents of E. nuda extract (ENE) and evaluate its antioxidant, antityrosinase, anticancer and antimicrobial activities. Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry analysis identified 33 compounds, 31 of which were reported for the first time, with phenols, terpenoids and carboxylic acids as dominant classes. ENE exhibited strong antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radicals with half-maximal inhibitory concentration (IC50) values of 40.42 ± 0.31 and 12.94 ± 0.22 µg/mL, respectively. Antimicrobial studies against six bacterial strains showed zones of inhibition ranging from 11 to 15 mm, with strong inhibitory activity against E. faecalis (minimum inhibitory concentration: 31.25 µg/mL). The extract demonstrated moderate antityrosinase activity (IC50: 357.36 µg/mL) compared to Kojic acid. Additionally, ENE showed significant antiproliferative effects against Panc-1, HepG2, and PC3 cancer cell lines, with IC50 values of 29.39, 38.13 and 46.97 µg/mL, respectively. These findings highlight the therapeutic potential of ENE, supported by its diverse phytoconstituents and bioactivities, paving the way for its development in both traditional and modern medicine.

Pre-pollination isolation by pollinator specificity: settling moth versus hawkmoth pollination in two sympatric Habenaria species (Orchidaceae)

BACKGROUND

Habenaria species typically produce green or white flowers, bear nectar spurs, emit crepuscular-nocturnal scents, and are usually pollinated by crepuscular/nocturnal moths. However, the roles of floral traits in pollinator differentiation contributing to reproductive success in sympatric Habenaria species require further definition. In this study, we investigated flowering phenology, floral traits, pollinator behavior, and reproductive success of two co-occurring and co-blooming Habenaria species (H. ciliolaris and H. schindleri) in southeastern China. We also conducted intraspecific and interspecific hand pollinations to determine their respective breeding systems and the extent of interspecific post-pollination isolation.

RESULTS

Both species are self-compatible but rely on pollinators for sexual reproduction. Habenaria ciliolaris was pollinated by two species of nocturnal, settling moths (Thinopteryx nebulosa and Porsica sp.). They foraged for nectar upside down or from one side, carrying pollinaria on their eyes because the curved lateral lobes of the labellum block the movements of settling moths on these flowers. Habenaria schindleri was pollinated by two crepuscular hawkmoths (Eupanacra mydon and Hippotion rafflesi), which carried pollinaria between their palpi while hovering in front of flowers while taking nectar. The proboscis lengths of pollinators of both Habenaria species matched the spur lengths of their corresponding flowers. Habenaria ciliolaris experienced a high level of inbreeding depression. Interspecific pollination by applying pollen grains from H. schindleri to the stigmas of H. ciliolaris, resulted in a low level of seed set.

CONCLUSIONS

Differences in floral morphology and nectar volume/concentration appear to contribute to segregating members of the pollinator guild of some Habenaria species. These findings offer new insights to our understanding of the partitioning of pollinators between co-blooming congeners in the Orchidaceae.

Tracking hidden dimensions of plant biogeography from herbaria

Plants are diverse, but investigating their ecology and evolution in nature across geographic and temporal scales to predict how species will respond to global change is challenging. With their geographic and temporal breadth, herbarium data provide physical evidence of the existence of a species in a place and time. The remarkable size of herbarium collections along with growing digitization efforts around the world and the possibility of extracting functional traits and geographic data from preserved plant specimens makes them invaluable resources for advancing our understanding of changing species distributions over time, functional biogeography, and conserving plant communities. Here, I synthesize core aspects of plant biogeography that can be gleaned from herbaria along changing distributions, attributes (functional biogeography), and conservation biogeography across the globe. I advocate for a collaborative, multisite, and multispecies research to harness the full potential of these collections while addressing the inherent challenges of using herbarium data for biogeography and macroecological investigations. Ultimately, these data present untapped resources and opportunities to enable predictions of plant species' responses to global change and inform effective conservation planning.

Unveiling a Meaningful Form of Cypripedium × ventricosum Sw. (Cypripedioideae, Orchidaceae) from Changbai Mountain, China: Insights from Morphological, Molecular, and Plastome Analyses

A Cypripedium plant was discovered in Wangqing County, Changbai Mountain, Jilin Province. This newly discovered plant of Cypripedium not only inhabits the same natural habitat as Cypripedium calceolus L. and Cypripedium × ventricosum Sw. but also has a morphology intermediate between that of C. calceolus and C. × ventricosum. Its dorsal sepals, petals, and synsepal are similar to those of C. calceolus, while the color of its lip is intermediate between that of C. calceolus and C. × ventricosum. For the purpose of distinguishing the newly discovered plant of Cypripedium from other Cypripedium plants, we provisionally named it W1. To further verify the taxonomic status of W1, we introduced three identified forms of C. × ventricosum and conducted molecular biology analyses with W1, C. calceolus, and C. × ventricosum. The analyses further confirmed the relationship between W1 and C. × ventricosum, and the phylogenetic analysis of the nuclear region demonstrated a close relationship between W1 and C. calceolus. Collectively, the morphological and molecular evidence indicates that W1 is a product of the backcross between C. × ventricosum and C. calceolus. Although it shows morphological differences from typical C. × ventricosum, it can still be considered a form of C. × ventricosum. We further investigated the chloroplast genome of this form of C. × ventricosum and determined that its total genome length was 196,850 bp. The genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. By analyzing the phylogenetic position and chloroplast genome of the form of C. × ventricosum, this study clarified the relationships among Cypripedium taxa with similar morphological characteristics, laying a foundation for research on orchid evolution and species conservation.

From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding

The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.

Factors Influencing Orchid Species Richness in the Central Balkans: The Importance of Belowground Organ Types

The Balkan Peninsula is considered one of the most important centres of orchid diversity in Europe. However, the patterns of orchid species richness in the Central Balkans have not been sufficiently studied so far. The aim of this study was, therefore, to identify the centres of orchid diversity and the factors that influence the spatial variation in orchid species richness in the Central Balkans. For the analyses, the area of the Central Balkans was divided into 10 × 10 km grid cells. The environmental variables determined for each grid cell and used in the analyses were altitude, bioclimatic variables, geological substrates and habitat types. A random forest (RF) analysis was used to identify the environmental predictors most strongly associated with species richness. In addition to the total number of taxa, orchids with three belowground organ types were analysed separately: (a) rhizomatous orchids, (b) orchids with palmately lobed and fusiform tubers ("palmate tuberous orchids") and (c) orchids with spherical or ovoid tubers ("ovoid tuberous orchids"). In the Central Balkans, 54 orchid species and subspecies have been recorded, and the most important centres of diversity are the Tara, Zvijezda, Jadovnik and Zlatar Mountains and the Ovčar-Kablar Gorge. In general, two groups of grid cells with the largest number of orchid taxa, i.e., hotspots, stood out: (1) grid cells with a large altitudinal range and (2) grid cells occupied by gorges and ravines. The most important gradients influencing orchid species richness are specific habitat types and altitudinal ranges, while climatic factors and geological substrates are less important. The most important factors affecting the richness of total and rhizomatous orchids are altitudinal range and habitat types (Abieti-Fagenion, Ostryo-Carpinion orientalis and Pinion nigrae forests), highlighting the important role of habitat heterogeneity. The maximum altitude, percentage of Abieti-Fagenion and Vaccinio-Picetea forests and the minimum value of the mean temperature of the driest quarter are the most important factors for determining the richness of palmate tuberous orchids, whereas the percentage of xero-thermophilous habitat types (Ostryo-Carpinion orientalis, Asplenietea trichomanis and Pinion nigrae) has the greatest influence on the richness of ovoid tuberous orchids. These results confirm the hypothesis concerning the origin and development of underground organs in orchids, emphasising that palmate tuberous orchids are best adapted to cold and humid habitat conditions, whereas ovoid tuberous orchids have the ability to grow in habitats with very warm and dry conditions. This study provides a good basis for better orchid conservation planning and underlines the importance of belowground strategies as a feature of orchid life history that should be considered when studying patterns of orchid diversity.

A Survey of Wild Indigenous Cryptostylis ovata Orchid Populations in Western Australia Reveals Spillover of Exotic Viruses

Cryptostylis ovata is a terrestrial orchid endemic to southwestern Australia. The virus status of C. ovata has not been studied. Eighty-three C. ovata samples from 16 populations were collected, and sequencing was used to identify RNA viruses from them. In one population, all tested plants were co-infected with isolates of the exotic-to-Australia viruses Ornithogalum mosaic virus (OrMV) and bean yellow mosaic virus (BYMV). In another population, one plant was infected with BYMV. No viruses were detected in the remaining populations. The OrMV isolate shared 98-99% nucleotide identity with isolates identified from wild indigenous Lachenalia (Iridaceae) plants in South Africa. This suggests that the source of OrMV in C. ovata may be one or more bulbous iridaceous flowering plants of southern African origin that were introduced to Western Australia as ornamentals and that have since become invasive weeds. One BYMV isolate from C. ovata also exhibited 99% nucleotide identity with strains isolated from the exotic leguminous crop Lupinus angustifolius in Western Australia, suggesting possible spillover to indigenous species from this source. This study with C. ovata highlights the probable role of invasive weeds and exotic crops as sources of exotic virus spillovers to indigenous plants.

Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia

BACKGROUND AND AIMS

Heterotrophic plants have long been a challenge for systematists, exemplified by the base of the orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species.

METHODS

Here we address the utility of organellar genomes in resolving relationships at the epidendroid base, specifically employing models of heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses of plastid genome evolution in heterotrophs and structural variation in matK.

KEY RESULTS

We present the first complete plastid genomes (plastomes) of Wullschlaegelia, the sole genus of the tribe Wullschlaegelieae, revealing a highly reduced genome of 37 kb, which retains a fraction of the genes present in related autotrophs. Plastid phylogenomic analyses recovered a strongly supported clade composed exclusively of mycoheterotrophic species with long branches. We further analysed mitochondrial gene sets, which recovered similar relationships to those in other studies using nuclear data, but the placement of Wullschlaegelia remains uncertain. We conducted comparative plastome analyses among Wullschlaegelia and other heterotrophic orchids, revealing a suite of correlated substitutional and structural changes relative to autotrophic species. Lastly, we investigated evolutionary and structural variation in matK, which is retained in Wullschlaegelia and a few other 'late stage' heterotrophs and found evidence for structural conservation despite rapid substitution rates in both Wullschlaegelia and the leafless Gastrodia.

CONCLUSIONS

Our analyses reveal the limits of what the plastid genome can tell us on orchid relationships in this part of the tree, even when applying parameter-rich heterotachy models. Our study underscores the need for increased taxon sampling across all three genomes at the epidendroid base, and illustrates the need for further research on addressing heterotachy in phylogenomic analyses.

Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

BACKGROUND AND AIMS

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time.

METHODS

We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.

KEY RESULTS

All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographical distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographical analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone probably occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the glacial cycles of the Pliocene-Quaternary may have contributed to further speciation and reticulate evolution within Cypripedium.

CONCLUSIONS

Our study provides novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Spatiotemporal Pattern of a Macrofungal Genus Phylloporia (Basidiomycota) Revealing Its Adaptive Evolution in China

The understanding of distribution and the evolutionary scenario is crucial for the utilization and conservation of biological resources; nevertheless, such explorations rarely focus on macrofungi. The current study selects a macrofungal genus, Phylloporia, and explores its spatiotemporal pattern in China. A total of 117 available occurrence records of Phylloporia in China were summarized for the current analyses. Ensemble modeling supports the highly suitable habitat of Phylloporia concentrated in southern, especially southeastern, China, where the ancestor of Phylloporia originated 77.74 million years ago and then dispersed to other parts of China. Benefitting from the available suitable habitats, Phylloporia rapidly diversified after its divergence in Southeast China. Then, the net diversification rate slowed down when the rapidly diversifying species filled available niches in Southeast China and the dispersed species in other parts of China inhabited the less suitable and unsuitable habitats. During adaptive evolution, precipitation, temperature and the host plant are the major environmental variables that shape the spatiotemporal pattern of Phylloporia. In conclusion, the current study reveals the adaptive evolutionary scenario of Phylloporia and provides the first exploration of the spatiotemporal pattern of macrofungi.

Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis

Asparagales, the largest monocot order, is renowned for its ecological, economic, and medicinal significance. Here, we leverage transcriptome data from 455 Asparagales species to explore the phylogeny of Asparagales. Moreover, we investigate the evolutionary patterns of the genes involved in allium flavor formation. We not only establish a robust bifurcating phylogeny of Asparagales but also explore their reticulate relationships. Notably, we find that eight genes involved in the biosynthesis of allium flavor compounds underwent expansion in Allium species. Furthermore, we observe Allium-specific mutations in one amino acid within alliinase and three within lachrymatory factor synthase. Overall, our findings highlight the role of gene expansion, increased expression, and amino acid mutations in driving the evolution of Allium-specific compounds. These insights not only deepen our understanding of the phylogeny of Asparagales but also illuminate the genetic mechanisms underpinning specialized compounds.

The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids

Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. In this study, we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83-Gb de novo genome with a scaffold N50 of 1.7 Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid terpene synthase genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids.

expowo: An R package for mining global plant diversity and distribution data

Premise

Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.

Methods and Results

The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.

Conclusions

By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.

Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)

Cypripedioideae (slipper orchids; Orchidaceae) currently consist of ∼200 herbaceous species with a strikingly disjunctive distribution in tropical and temperate regions of both hemispheres. In this study, an updated phylogeny with representatives from all five cypripedioid genera was presented based on maximum likelihood and Bayesian inference of plastome and low-copy nuclear genes. Phylogenomic analyses indicated that each genus is monophyletic, but some relationships (e.g., those among Cypripedium sects. Acaulia, Arietinum, Bifolia, Flabellinervia, Obtusipetala and Palangshanensia) conflict with those in previous studies based on Sanger data. Cypripedioideae appeared to have arisen in South America and/or the adjacent Qinghai-Tibet Plateau and Hengduan Mountains ∼35 Mya. We inferred multiple dispersal events between East Asia and North America in Cypripedium, and between mainland Southeast Asia and the Malay Archipelago in Paphiopedilum. In the Americas, divergences among four genera (except Cypripedium) occurred around 31-20 Mya, long before the closure of the Isthmus of Panama, indicating the importance of long-distance dispersal. Evolutionary patterns between morphological and plastome character evolution suggested several traits, genome size and NDH genes, which are likely to have contributed to the success of slipper orchids in alpine floras and low-elevation forests. Species diversification rates were notably higher in epiphytic clades of Paphiopedilum than in other, terrestrial cypripedioids, paralleling similar accelerations associated with epiphytism in other groups. This study also suggested that sea-level fluctuations and mountain-building processes promoted the diversification of the largest genera, Paphiopedilum and Cypripedium.

The Complete Mitogenome of Apostasia fujianica Y.Li & S.Lan and Comparative Analysis of Mitogenomes across Orchidaceae

Apostasia fujianica belongs to the genus Apostasia and is part of the basal lineage in the phylogenetic tree of the Orchidaceae. Currently, there are only ten reported complete mitochondrial genomes in orchids, which greatly hinders the understanding of mitochondrial evolution in Orchidaceae. Therefore, we assembled and annotated the mitochondrial genome of A. fujianica, which has a length of 573,612 bp and a GC content of 44.5%. We annotated a total of 44 genes, including 30 protein-coding genes, 12 tRNA genes, and two rRNA genes. We also performed relative synonymous codon usage (RSCU) analysis, repeat sequence analysis, intergenomic transfer (IGT) analysis, and Ka/Ks analysis for A. fujianica and conducted RNA editing site analysis on the mitochondrial genomes of eight orchid species. We found that most protein-coding genes are under purifying selection, but nad6 is under positive selection, with a Ka/Ks value of 1.35. During the IGT event in A. fujianica's mitogenome, the trnN-GUU, trnD-GUC, trnW-CCA, trnP-UGG, and psaJ genes were identified as having transferred from the plastid to the mitochondrion. Compared to other monocots, the family Orchidaceae appears to have lost the rpl10, rpl14, sdh3, and sdh4 genes. Additionally, to further elucidate the evolutionary relationships among monocots, we constructed a phylogenetic tree based on the complete mitogenomes of monocots. Our study results provide valuable data on the mitogenome of A. fujianica and lay the groundwork for future research on genetic variation, evolutionary relationships, and breeding of Orchidaceae.

Genome-Wide Identification and Expression Pattern Analysis of GATA Gene Family in Orchidaceae

The GATA transcription factors play crucial roles in plant growth, development, and responses to environmental stress. Despite extensive studies of GATA genes in many plants, their specific functions and mechanisms in orchids remain unexplored. In our study, a total of 149 GATA genes were identified in the genomes of seven sequenced orchid species (20 PeqGATAs, 23 CgGATAs, 24 CeGATAs, 23 DcaGATAs, 20 DchGATAs, 27 DnoGATAs, and 12 GelGATAs), classified into four subfamilies. Subfamily I typically contains genes with two exons, while subfamily II contains genes with two or three exons. Most members of subfamilies III and IV have seven or eight exons, with longer introns compared to subfamilies I and II. In total, 24 pairs (CgGATAs-DchGATAs), 27 pairs (DchGATAs-DnoGATAs), and 14 pairs (DnoGATAs-GelGATAs) of collinear relationships were identified. Cis-acting elements in GATA promoters were mainly enriched in abscisic acid (ABA) response elements and methyl jasmonate (MeJA) elements. Expression patterns and RT-qPCR analysis revealed that GATAs are involved in the regulation of floral development in orchids. Furthermore, under high-temperature treatment, GL17420 showed an initial increase followed by a decrease, GL18180 and GL17341 exhibited a downregulation followed by upregulation and then a decrease, while GL30286 and GL20810 displayed an initial increase followed by slight inhibition and then another increase, indicating diverse regulatory mechanisms of different GATA genes under heat stress. This study explores the function of GATA genes in orchids, providing a theoretical basis and potential genetic resources for orchid breeding and stress resistance improvement.

Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera

PREMISE

Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants.

METHODS

Using floral tissue from an herbarium specimen, we sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities.

RESULTS

The plastome is the most reduced of those sequenced among the orchid subfamily Orchidoideae. In Degranvillea, it has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and of correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae.

CONCLUSIONS

Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.

Progress in systematics and biogeography of Orchidaceae

Orchidaceae are one of the largest families of angiosperms in terms of species richness. In the last decade, numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These studies have provided new insights into the systematics, diversification and biogeography of Orchidaceae, establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding the precise placement of certain lineages within these phylogenetic frameworks. To address these discrepancies and deepen our understanding of the phylogenetic structure of Orchidaceae, we provide a comprehensive overview and analysis of phylogenetic studies focusing on contentious groups within Orchidaceae since 2015, delving into discussions on the underlying reasons for observed topological conflicts. We also provide a novel phylogenetic framework at the subtribal level. Furthermore, we examine the tempo and mode underlying orchid species diversity from the perspective of historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, we delineate avenues for future research aimed at enhancing our understanding of Orchidaceae phylogeny and diversity.

Evolution of Whirly1 in the angiosperms: sequence, splicing, and expression in a clade of early transitional mycoheterotrophic orchids

The plastid-targeted transcription factor Whirly1 (WHY1) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study of autotrophic losses across the angiosperms. While gene loss in the plastid and nuclear genomes has been well studied in mycoheterotrophic plants, the evolution of the molecular mechanisms impacting genome stability is completely unknown. Here, we characterize the evolution of WHY1 in four early transitional mycoheterotrophic orchid species in the genus Corallorhiza by synthesizing the results of phylogenetic, transcriptomic, and comparative genomic analyses with WHY1 genomic sequences sampled from 21 orders of angiosperms. We found an increased number of non-canonical WHY1 isoforms assembled from all but the greenest Corallorhiza species, including intron retention in some isoforms. Within Corallorhiza, phylotranscriptomic analyses revealed the presence of tissue-specific differential expression of WHY1 in only the most photosynthetically capable species and a coincident increase in the number of non-canonical WHY1 isoforms assembled from fully mycoheterotrophic species. Gene- and codon-level tests of WHY1 selective regimes did not infer significant signal of either relaxed selection or episodic diversifying selection in Corallorhiza but did so for relaxed selection in the late-stage full mycoheterotrophic orchids Epipogium aphyllum and Gastrodia elata. Additionally, nucleotide substitutions that most likely impact the function of WHY1, such as nonsense mutations, were only observed in late-stage mycoheterotrophs. We propose that our findings suggest that splicing and expression changes may precede the selective shifts we inferred for late-stage mycoheterotrophic species, which therefore does not support a primary role for WHY1 in the transition to mycoheterotrophy in the Orchidaceae. Taken together, this study provides the most comprehensive view of WHY1 evolution across the angiosperms to date.

Morphological and Ultrastructural Features of Selected Epidendroideae Pollen Dispersal Units and New Insights into Their Chemical Nature

Orchidaceae display enormous diversity in their flower morphology, which is particularly evident in their pollen dispersal units (pollinia, pollinaria). The packaging of pollen by elastoviscin leads to a great diversity of these morphologically and structurally complex pollen units. Despite being one of the most diverse angiosperm families, the available palynological data on orchids remain limited and sometimes contradicting. This study provides new insights into the pollen morphology and ultrastructure of five orchid species from the subfamily Epidendroideae, using combined light, scanning electron, and transmission electron microscopy. The aim was to compare the morphology and ultrastructure of pollen dispersal units and to elucidate the chemical nature of the pollen wall layers and of elastoviscin. Our combined light and electron microscopy investigation demonstrated the presence of six tetrad types even within a single pollinium, which is unique for orchids. The application of different staining methods confirmed the assumed lipidic nature of elastoviscin and the differences in its contrast and ultrastructure suggest a mixture of sticky materials with dissimilar chemical compositions. This study affirmed that sporopollenin is mostly restricted to the outer pollen grains of peripheral tetrads in compact and sectile pollinia, while inner tetrads exhibit highly reduced non-sporopollenin pollen walls.