OrchidBase 5.0: updates of the orchid genome knowledgebase.

Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/.

Goodyeramedogensis (Orchidaceae), a new species from Tibet, China.

A new species of Goodyera (Orchidaceae) from Tibet, China, G.medogensis, is described and illustrated here. Molecular phylogenetic results based on one nuclear (ITS) and two plastid markers (matK and trnL-F) support the recognition of G.medogensis as a new species in GoodyerasubsectionReticulum. Morphologically, the novelty is most similar to G.biflora, G.vittata and especially to G.hemsleyana, but differs by the thick grid lines of the reticulations with a diffused margin on the adaxial surface of the leaf blades, the inflorescence with more flowers, the obliquely obovate-rhombic petals, the yellow or yellowish labellum without a lamella on the blade, and the shorter trichomes on the floral bracts, sepals and ovary. Finally, a key to the species of Goodyerasubsect.Reticulum in China is also provided.

Seed morphometry and ultrastructure studies on some Turkish orchids (Orchidaceae).

Orchid seeds have great morphological variations that imply the phylogenetic relationship of the species depending on the biodiversity of the family or act as an adaptation to seed dispersal mechanisms depending on the life form. This study aims to both describe and analyse the qualitative and quantitative traits of 12 Turkish orchids representing epidendroids and orchidoids in detail to investigate which properties are diagnostic among these taxa and also reveal if seed properties are differentiated in relationship to the ecological preferences of the studied species. Both qualitative and quantitative features were determined, and measurements were obtained using light and scanning electron microscopy. We applied the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis and canonical discriminant analysis to the qualitative and quantitative traits. Furthermore, we analyzed the same orchid seed in correlation with ecological traits such as habitats and the elevation preferences of species. This study confirmed the usefulness of both data sets for effectively assessing the variation of orchid seeds. Although the seed characters such as the cell shape differences in the chalazal or medial region, seed sizes, cell numbers on the longitudinal axis, and periclinal wall ornamentation are taxonomically conserved, some other characteristics such as seed shape, the absence of periclinal wall ornamentation, and larger embryo size imply ecological adaptation or developmental achievement for germination. This study confirms the diagnostic value of both qualitative and quantitative seed features, which are effective in explaining the orchid seed variety.

Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role.

We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.

The effect of seasonality on developmental stages of anthetic ovule integuments in Mediterranean orchids.

Orchids, differently from most flowering plants, have under-differentiated ovules at anthesis that require pollination to complete differentiation. This ovule developmental stage has been often observed in tropical species in which the absence of an evident seasonality may allow plants to extend their phenology beneficiating of a long time for post-pollination events. Here, we used scanning electron microscopy (SEM) to detect ovule integument developmental stages in 21 species of Mediterranean Orchidoideae and Epidendroideae and in 11 tropical Epidendroideae with the aim of understanding whether species with a seasonal constraint and shorter time for post-pollination ovule maturation are characterized by different stages of ovule development at anthesis. We found that Mediterranean orchids (both Orchidoideae and Epidendroideae) have more developed ovule integuments than tropical orchids. Most species show partially to fully developed ovules at anthesis with the exception of Cephalanthera where ovules are arrested in a very early developmental stage. Despite the phylogenetic signal, anthetic ovule integument development differs between related species (with different pollination strategies or blooming times), suggesting the presence of some ecological constraints. The synchronization between ovule integuments and megagametophyte development, as found in tropical orchids, is also confirmed in Mediterranean orchids. Our data show that Mediterranean and tropical orchids clearly differ in anthetic ovule developmental stages, likely depending on seasonality.

Comparative anatomical properties of some Epidendroideae and Orchidoideae species distributed in NE Turkey.

In this research, anatomical, leaf micromorphological features of the samples belonging to 25 taxa (Anacamptis Rich., Cephalanthera Rich., Dactylorhiza Necker ex Nevski, Gymnadenia R.Br., Himantoglossum Spreng., Limodorum Boehm., Ophrys L., Orchis L., Platanthera Rich., Serapias L., Spiranthes Rich. and Steveniella Schltr.) spread in the Karadeniz Region have been evaluated comparatively. In anatomical studies, the transverse section from root, stem and leaf, and surface section from leaves of plants were examined. In addition, micromorphological properties of leaf were determined by electron microscopy. Morphometrical analyses were carried out using the anatomical and leaf micromophological characters of each taxa. The data matrices were obtained by examining the results of at least three samples collected from different localities. The data were evaluated using Statistical Package for the Social Sciences (SPSS) and PAleontological STatistics (PAST) statistical programs with PCA, linear discriminant analysis (LDA), and unweighted pair group method with arithmetic mean analysis. Anatomical characteristics of plants such as root epidermis cell length, cortex diameter and pith cell diameter, leaf upper epidermis length-width and bulliform cell length-width were determined to be important characteristics. It was concluded that these characters are especially important in grouping at the genus level.

The complete chloroplast genome sequence of Platanthera chlorantha (Orchidaceae).

Here, we report the first complete chloroplast genome of Platanthera chlorantha (Orchidaceae: Orchidoideae). The circular genome with the length of 154,260 bp possesses the typical structure consisting of a large single copy region (LSC) of 83,279 bp and a small single copy region (SSC) of 17,759 bp, separated from each other by two copies of inverted repeats (IRs) of 26,611 bp. The plastome encodes 134 genes, of which 88 were protein-coding, eight encoded ribosomal RNA, and 38 transfer RNAs. The overall GC content was 36.74%. The plastome sequence provided here constitutes a valuable resource for analyzing genetic diversity of the Orchidaceae family.

The complete chloroplast genome sequence of Platanthera minor.

Platanthera minor is widely distributed in East Asia. The complete circular chloroplast genome with a length of 154,430 bp possesses the typical structure, consisting of a large single copy (LSC) of 83,536 bp, a small single copy (SSC) of 17,612 bp, and two inverted repeats (IR) of 26,641 bp. The average GC content of the genome is 36.7%. The circular P. minor chloroplast genome contains 114 genes, including 80 protein-coding genes, four rRNA genes, and 30 tRNA genes. The chloroplast sequence provided a resource for analyzing genetic diversity of the Orchidaceae family.

Complete plastid genome of Cheirostylis chinensis (Orchidaceae, Goodyerinae).

The first complete plastid genome of Cheirostylis, Ch. chinensis, was assembled and analyzed in this study. The total genome was 147,218 bp in length, consisting of a large single-copy region (LSC) of 81,081 bp, a small single-copy region (SSC) of 14,769 bp, and two inverted repeat regions (IRA and IRB) of 25,684 bp. The genome contained 131 genes, including 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes. Phylogenomic analysis indicated that Ch. chinensis nested within Goodyerinae.