Phylogenetic position and plastid genome structure of Vietorchis, a mycoheterotrophic genus of Orchidaceae (subtribe Orchidinae) endemic to Vietnam.

The orchid genus Vietorchis comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, V. aurea, occurs in a single location in northern Vietnam within a lowland limestone karstic area. Vietorchis furcata and V. proboscidea, in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of Vietorchis remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of Vietorchis (V. aurea and V. furcata) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of Vietorchis into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between Vietorchis and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. Vietorchis is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, Vietorchis is sister to the photosynthetic genus Sirindhornia. Sirindhornia is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for Vietorchis. Flower morphology is concordant with the molecular data in placing Vietorchis into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, Vietorchis shows no close structural similarity with any of its genera; in particular, the proximity between Vietorchis and Sirindhornia has never been proposed. Finally, we assembled the plastid genome of V. furcata, which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of Vietorchis lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected.

A new species and a replacement name in Cynanchum (Apocynaceae, Asclepiadeae) from China.

Cynanchumpingtaoi S.Jin Zeng, G.D.Tang & Miao Liao, sp. nov. (Apocynaceae) from Yunnan Province, China, is described and illustrated based on morphological and molecular evidence. Its deeply cordate to reniform leaves and campanulate, large flowers show that it is a member of former Raphistemma Wall., which has been included in Cynanchum L.. It is different from all former Raphistemma species by the broadly ovate corolla lobes, purple-red corolla and connivent corona tip slightly exceeding the corolla throat. Meanwhile, Cynanchumlonghushanense G.D.Tang & Miao Liao, nom. nov. is proposed as replacement name for Raphistemmabrevipedunculatum Y.Wan, which was considered a synonym of Cynanchumhooperianum (Blume) Liede & Khanum but is here reinstated as a distinct species because of significant morphological differences.

Parahellenia, a new genus segregated from Hellenia (Costaceae) based on phylogenetic and morphological evidence.

Previous studies recognized three major lineages of the family Costaceae: a South American clade, an Asian clade and a Costus clade. However, the genus Hellenia within the Asian clade has been shown to be non-monophyletic and its morphology has not been studied carefully. Therefore, the complete plastid genomes of Hellenia species were obtained and the monophyly of Hellenia was tested through four different datasets in this study. Plastid phylogenomic analyses of Costaceae revealed that Hellenia is strongly supported as paraphyletic. Two major clades are recovered, namely the Hellenia s.s. subclade and the Parahellenia subclade. Phylogenetic analyses based on an enlarged taxon sampling of the Asian clade using a two chloroplast markers dataset (trnK intron and trnL-F spacer) confirmed the paraphyly of Hellenia. Meanwhile, morphological analyses suggested that members of the Parahellenia subclade differ from the remaining Hellenia species in many characters including inflorescences, bracts, stigma, axillary buds, floral tubes and labellum. According to the present molecular and morphological evidence, the latter subclade is recognized as a new genus, Parahellenia. Two new species are described, four new combinations are made, and identification keys are also provided.

Fordiophytontereticaule (Melastomataceae), a new species from China.

A new species, Fordiophytontereticaule, from China, is described and illustrated here based on morphological and molecular evidence. It is morphologically similar to F.faberi in having erect stems, slightly oblique and membranous leaf blades, broadly ovate to suborbicular bracts, and oblong petals, but differs by the terete stems, densely puberulous petioles, and elliptic leaf blades. Our phylogenetic analyses based on plastid genome and nrITS data indicate that this new species is clustered with four Fordiophyton species of Yunnan but placed far apart from F.faberi. An updated key to the genus is also provided.

Tigridiopalma exalata, a new and endangered species of Melastomataceae from China.

A new species of the genus Tigridiopalma, formerly considered monotypic, is here described as T. exalata and illustrated based on molecular and morphological evidence. It is morphologically similar to T. magnifica in having a short stem, huge basal leaves, scorpioid cymes, and 5-merous flowers, but differs in having ribbed and pale yellow puberulent petioles, purple petals with a small white apical patch, connectives of longer stamens with a distinct dorsal short spur at their base, and wingless capsules. Due to the restricted distribution, small populations and horticultural potential of this new species, it should be categorized as an Endangered species (EN).

Complete plastome sequence of Hoya carnosa (L. f.) R. Br. (Apocynaceae).

Hoya is a remarkable genus with high horticultural ornamental value. In this study, we report and characterize the complete plastid genome sequence of Hoya carnosa. The complete chloroplast genome was 176,340 bp in length, which includes a pair of inverted repeat regions (IRs) of 41,381 bp separated by a large single copy region (LSC) 91,281 bp and a small single copy region (SSC) 2,297 bp. Interestingly, IRs expanded into SSC, with the result that most of the genes in SSC were duplicated. This chloroplast genome contained 110 genes, including 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The complete plastome sequence of H. carnosa will provide some useful information for future phylogenetic study of Hoya and its horticultural application.

Author Correction: The Apostasia genome and the evolution of orchids.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Characterization of the complete chloroplast genome sequence of Blastus cochinchinensis (Melastomataceae).

Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (B. cochinchinensis). The complete chloroplast genome (cp) size of B. cochinchinensis was 156,005 bp in length, containing a pair of 26,812 bp inverted repeat (IR) regions, which were separated by a large single-copy region (LSC) 85,926 bp and a small single-copy (SSC) region 16,455 bp. The overall GC content of the genome was 37.0%. The whole genome contained 129 unique genes, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that B. cochinchinens was sister to Barthea barthei. The present study provided B. cochinchinensis genomic information that may be found useful in conservation and molecular phylogenetic studies on Blastus.

The complete chloroplast genome sequence of monotypic Cyphotheca (Melastomataceae), an endemic genus in China.

Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as 'Near Threatened (NT)' by IUCN Red List of China. Herein, we report the complete chloroplast genome (cpDNA) sequence assembled from Illumina pair-end sequencing data. The complete chloroplast genome was 156,424 bp in length, which includes two inverted repeat regions (IRs) of 26,776 bp each, which were separated by a large single copy region (LSC) 85,900 bp and a small single copy region (SSC) 16,972 bp. The chloroplast genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content in the chloroplast genome of C. montana was 37.0%. The phylogenomic analysis showed that C. montana is sister to Barthea barthei.

The Apostasia genome and the evolution of orchids.

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.