Subtribe Aeridinae Research Articles

The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships

Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report the chloroplast genome sequence of Taeniophyllum complanatum, including an extensive comparative analysis with other types of leafless orchids. The chloroplast genome of T. complanatum exhibited a typical quadripartite structure, and its overall structure and gene content were relatively conserved. The entire chloroplast genome was 141,174 bp in length, making it the smallest known chloroplast genome of leafless epiphytic orchids. It encoded a total of 120 genes, including repetitive genes, comprising 74 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted on the chloroplast genomes of 43 species belonging to five subfamilies of Orchidaceae. The results showed that the five subfamilies were monophyly, with nearly all segments having a 100% bootstrap value. T. complanatum and Chiloschista were clustered together as a sister group to Phalaenopsis and occupied the highest position in the Epidendroideae. Phylogenetic analysis suggested that T. complanatum and other leafless orchids within the Orchidaceae evolved independently. This study may provide the foundation for research on phylogenetic and structural diversity in leafless epiphytic orchids, thereby enhancing the resources available for chloroplast genome studies in Orchidaceae.

Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata

BackgroundThe disputed phylogenetic position of Aerides flabellata Rolfe ex Downie, due to morphological overlaps with related species, was investigated based on evidence of complete chloroplast (cp) genomes. The structural characterization of complete cp genomes of A. flabellata and A. rosea Lodd. ex Lindl. & Paxton were analyzed and compared with those of six related species in “Vanda-Aerides alliance” to provide genomic information on taxonomy and phylogeny.ResultsThe cp genomes of A. flabellata and A. rosea exhibited conserved quadripartite structures, 148,145 bp and 147,925 bp in length, with similar GC content (36.7 ~ 36.8%). Gene annotations revealed 110 single-copy genes, 18 duplicated in inverted regions, and ten with introns. Comparative analysis across related species confirmed stable sequence identity and higher variation in single-copy regions. However, there are notable differences in the IR regions between two Aerides Lour. species and the other six related species. The phylogenetic analysis based on CDS from complete cp genomes indicated that Aerides species except A. flabellata formed a monophyletic clade nested in the subtribe Aeridinae, being a sister group to Renanthera Lour., consistent with previous studies. Meanwhile, a separate clade consisted of A. flabellata and six Vanda R. Br. species was formed, as a sister taxon to Holcoglossum Schltr.ConclusionsThis research was the first report on the complete cp genomes of A. flabellata. The results provided insights into understanding of plastome evolution and phylogenetic relationships of Aerides. The phylogenetic analysis based on complete cp genomes showed that A. flabellata should be placed in Vanda rather than in Aerides.

Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation.

Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia.

Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes

BackgroundChiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation.ResultsWe are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU–rpl32 > rpoB–trnCGCA > psbK–psbI > psaC–rps15 > trnEUUC–trnTGGU > accD–psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47–56 SSRs and 11–14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support.ConclusionThis study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.

Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae)

Subtribe Aeridinae (Vandeae, Epidendroideae, Orchidaceae) consists of 83 genera and 2,345 species. The present study completely decoded the plastomes and nuclear ribosomal (nr) RNA gene clusters of seven species of Aeridinae belonging to Gastrochilus, Neofinetia, Pelatantheria, and Thrixspermum and compared them with existing data to investigate their genome evolution and phylogeny. Although no large structural variations were observed among the Aeridinae plastomes, 14 small inversions (SI) were found in Orchidaceae for the first time. Therefore, the evolutionary trends and usefulness of SI as molecular identification markers were evaluated. Since all 11 ndh genes in the Aeridinae plastome were lost or pseudogenized, the evolutionary trends of ndh genes are discussed at the tribe and family levels. In the maximum likelihood tree reconstructed from 83 plastome genes, the five Orchidaceae subfamilies were shown to have diverged in the following order: Apostasioideae, Vanilloideae, Cypripedioideae, Orchioideae, Epidendroideaeae. Divergence times for major lineages were found to be more recent, 5–10 Mya, than previous studies, which only used two or three genes. Vandeae, which includes Aeridinae, formed a sister group with Cymbidieae and Epidendreae. The Vandeae, Cymbidieae, and Epidendreae lineages were inferred to have diverged at 25.31 Mya; thus, numerous speciation events within Aeridineae occurred since then. Furthermore, the present study reconstructed a phylogenetic tree from 422 nrITS sequences belonging to Aerdinae and allied taxa and uses it to discuss the phylogenetic positions and species identities of five endangered species.

A new epiphytic species of Gastrochilus (Orchidaceae: Epidendroideae) from Yunnan, China

Gastrochilus Don (1825: 32.), subtribe Aeridinae (Orchidaceae), includes about 50 species, distributed from Southeast Asia to the Himalayas (Lucksom 2003, Jin et al. 2007, Shakya & Shrestha 2007, Chen et al. 2009). Generally, it is characterized by a saccate hypochile and two porate pollinia (Tsi et al. 1999). In China, about 30 species are found according to the most recent revision and recently published new species (Chen et al. 2009, Yi et al. 2010, Liu et al. 2016, Liu & Gao 2018).

Complete plastid genome of Vanda concolor (Orchidaceae, Aeridinae)

Vanda is one of the five most horticulturally important genera in Orchidaceae. In this study, we assembled the complete plastid genome of an important cultivated species, V. concolor. The plastome was 149,474 bp in length, containing a large single-copy region (LSC) of 85,678 bp, a small single-copy region (SSC) of 12,002 bp, and two inverted repeat regions (IR) of 25,897 bp. A total of 127 genes were predicted, including 38 tRNA, 8 rRNA, and 74 protein-coding genes. Phylogenetic analysis of 21 representative plastome of the subtribe Aeridinae suggested V. concolor to be sister to V. brunnea and that this pair is sister to Neofinetia.

The chloroplast genome of an Endangered orchid species, Gastrochilus calceolaris (Orchidaceae: Aeridinae)

This study reported the complete chloroplast genome of a critically Endangered Orchidaceae species Gastrochilus calceolaris and its phylogenetic position in subtribe Aeridinae based on 12 orchid species plastomes. The plastome of G. calceolaris, with a 148,428 bp size, consisted of a pair of inverted repeat regions of 25,950 bp, a small single copy region of 11,139 bp, and a large single copy region of 85,389 bp. G + C content was 36.8%. The phylogenetic analysis highly supported the sisterhood between Gastrochilus and Pelatantheria and a monophyletic Gastrochilus group comprising of G. calceolaris, G. fuscopunctatus, and G. japonicus.

Potential pollinator of Vanda falcata (Orchidaceae): Theretra (Lepidoptera: Sphingidae) hawkmoths are visitors of long spurred orchid

Vanda falcata is a species of orchid native to China, Korea and Japan. While it is arguably one of the most celebrated orchids in Japan there is no information on its pollinators. Although most species of the subtribe Aeridinae, to which V. falcata belongs, have a short spur, V. falcata has a long spur. The results of the current study provide strong evidence that V. falcata is pollinated by long-tongued hawkmoths (Theretra spp.), which indicates that the evolution of long spurs in V. falcata could be an adaptation to pollination by long-tongued moths.

A molecular phylogeny of Aeridinae (Orchidaceae: Epidendroideae) inferred from multiple nuclear and chloroplast regions

The subtribe Aeridinae, which contains approximately 90 genera, is one of the most diverse and taxonomically puzzling groups in Orchidaceae. In the present study, the phylogenetic relationships of Aeridinae were reconstructed utilizing five DNA sequences (ITS, atpI-H, matK, psbA-trnH, and trnL-F) from 211 taxa in 74 genera. The results of the phylogenetic analyses indicate that Aeridinae is monophyletic and that the subtribe can primarily be grouped into 10 clades: (1) Saccolabium clade, (2) Chiloschista clade, (3) Phalaenopsis clade, (4) Thrixspermum clade, (5) Vanda clade, (6) Aerides clade, (7) Trichoglottis clade, (8) Abdominea clade, (9) Gastrochilus clade, and (10) Cleisostoma clade. In our examination, most genera of Aeridinae were well-supported as monophyletic, and several genera, namely, Pteroceras, Cleisostoma, Vandopsis, Diploprora, Malleola, and Robiquetia, were found to be polyphyletic as currently circumscribed. In addition, several classifications of intra-genera, such as the subgenus Codonosepalum of Taeniophyllum and the section Gastrochilus of Gastrochilus, were also revealed to be paraphyletic. Due to the many questions raised by our phylogenies, the present study may serve as a reference for future taxonomic studies of Aeridinae.

New combinations in Aeridinae (Orchidaceae)

New combinations are made in the genera Arachnis, Brachypeza, Dimorphorchis, Grosourdya, Phalaenopsis, Renanthera, Robiquetia, Taeniophyllum, Thrixspermum, Trachoma and Trichoglottis. Two new subgenera are established in Phalaenopsis (subgen. Ornithochilus and Hygrochilus). These changes are proposed to begin aligning the genera recognized in subtribe Aeridinae with results of recent DNA analyses (published elsewhere).

A New Molecular Phylogeny and a New Genus, Pendulorchis, of the Aerides–Vanda Alliance (Orchidaceae: Epidendroideae)

BackgroundThe Aerides–Vanda alliance is a complex group in the subtribe Aeridinae (subfamily Epidendroideae, Orchidaceae). Some phylogenetic systems of this alliance have been previously proposed based on molecular and morphological analyses. However, several taxonomic problems within this alliance as well as between it and its allies remain unsolved.Methodology/Principal FindingsWe utilized ITS and five plastid DNA regions in this phylogenetic analysis. Consensus trees strongly indicate that the Aerides–Vanda alliance is monophyletic, and the 14 genera of this alliance can be grouped into the following clades with 14 subclades: 1. Aerides, comprising two subclades: Rhynchostylis and Aerides; 2. Ascocentropsis; 3. Papilionanthe; 4. Vanda, comprising five subclades: Neofinetia, Christensonia, Seidenfadenia, Ascocentrum, and Vanda–Trudelia, in which Vanda and Trudelia form a subclade; 5. Tsiorchis, comprising three subclades: Chenorchis, Tsiorchis, and two species of Ascocentrum; 6. Paraholcoglossum; and 7. Holcoglossum. Among the 14 genera, only Ascocentrum is triphyletic: two species of the Ascocentrum subclade, an independent subclade Ascocentrum subclade in the Tsiorchis clade; the Ascocentrum subclade in the Vanda clade; and one species in the Holcoglossum clade. The Vanda and Trudelia species belong to the same subclade. The molecular conclusion is consistent with their morphological characteristics.ConclusionsWe elucidate the relationship among the 14 genera of the Aerides–Vanda alliance. Our phylogenetic results reveal that the Aerides–Vanda alliance is monophyletic, but it can be divided into 14 genera. The data prove that Ascocentrum is triphyletic. Plants with elongate-terete leaves and small flowers should be treated as a new genus, Pendulorchis. Saccolabium himalaicum (Ascocentrum himalaicum) should be transferred to Pendulorchis. Ascocentrum pumilum, endemic to Taiwan, should be transferred to Holcoglossum. A new combination, Holcoglossum pumilum, was also established. Trudelia should not be recognized as an independent genus. Two new species, Pendulorchis gaoligongensis and Holcoglossum singchianum, were described as well.

Phylogeny of Subtribe Aeridinae (Orchidaceae) Inferred from DNA Sequences Data : Advanced Analyses Including Australasian Genera

Advanced phylogenetic analyses of the orchid subtribe Aeridinae has been conducted using DNA sequences of ITS region of nrDNA andmatK of cpDNA. In the preliminary work, we only involved the most representative Asian genera of the subtribe. Further, to establish more robust relationships in the Aeridinae, in this study we have extended the sampling to include Australasian specimens. Our analyses revealed that: (1) the subtribe is reorganised by four major groups with 11 subgroups (This is inconsistent with previous classification systems of the subtribe); (2) the Australasian region is a secondary center of diversification of the subtribe; (3) vegetative features have shown to have greater value than reproductive one in determining major groups in the subtribe; and (4) at genus level, some genera, i.e. Phalaenopsis,Cleisostoma, Sarcochilus, and Aerides are shown to be non-monophyletic. This study also resolved the taxonomic status ofAerides flabellata Rolve ex Downie, a species with a debatable generic position.

<p class="HeadingRunIn"><strong>New combinations in the genus <em>Vanda</em> (Orchidaceae)</strong></p>

A number of new combinations of names in subtribe Aeridinae are needed to bring species nomenclature for Vanda into alignment with recent phylogenetic analyses and a treatment to be published in a forthcoming volume of Genera orchidacearum. I present 17 name transfers from Ascocentrum, Ascocentropsis, Christensonia, Eparmatostigma, and Neofinetia to Vanda or indicate where there are existing epithets combined previously in Vanda.

New taxa of Philippine <i>Trichoglottis</i> Blume (Orchidaceae)

Trichoglottis Blume, a genus of monopodial orchids, belongs to the subtribe Aeridinae and has a distributional range from the Nicobar Islands to the Solomon Islands. It is comprised of about 60-64 species, with 89% endemism in the Malesian region (Schuiteman, 1999). There are 23 species in Borneo, 16 in Sumatra, 10 in Java, eight in the Malay Peninsula, two in the Lesser Sunda Islands, five in Sulawesi, three in the Moluccas, and two in New Guinea. Agoo et al . (2003) lists 23 species and five varieties in the Philippines. This follows the taxonomic treatment of Williams (1938) which considers Staurochilus and Stauropsis as congeneric with Trichoglottis . T. intermedia, a new species discovered by Williams, shows a combination of characteristics of both Staurochilus and Trichoglottis such as erect habit, short inflorescence and small flowers. In a taxonomic revision of the genus undertaken by Agoo (2002), which is mainly based on morphological, anatomical, and palynological evidence, three taxa were recognized as distinct and here proposed as new, i.e. T. apoensis subsp. alba, T. intermedia var . marginata , and T. mindanaensis f. lutea. DOI = 10.3860/psci.v43i0.369 Philipp. Scient. 43: 34-42 2007

Evolutionary analysis of pollinaria morphology of subtribe Aeridinae (Orchidaceae)

HIDAYAT, TOPIK; YUKAWA, TOMOHISA; ITO, MOTOMI. 2006. Evolutionary analysis of pollinaria morphology of subtribe Aeridinae (Orchidaceae). Reinwardtia 12(3): 223–235.–– Pollinarium is one of the distinct synapomorphies of Orchidaceae. With using characters derived from the pollinarium, phylogenetic relationships among genera of subtribe Aeridinae was examined. Cladistic analysis showed that (1) Subtribe Aeridinae is monophyletic group. (2) Five of six groups constructed in the analysis are consistent with the groups recognized in previous molecular phylogenetic analyses.(3)The genera Cleisostoma and Phalaenopsis are non-monophyletic group.(4) Pollinarium morphology endorses monophyly Trichoglottis and Phalaenopsis alliances. (5) Although transformation of the stipe and viscidium shapes in the subtribe is subjected to parallelism, the results showed that these characters are much useful in determining relationships in the subtribe than those of pollinium.

Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences

We conducted phylogenetic analyses using two DNA sequence data sets derived from matK, the maturase-coding gene located in an intron of the plastid gene trnK, and the internal transcribed spacer region of 18S-26S nuclear ribosomal DNA to examine relationships in subtribe Aeridinae (Orchidaceae). Specifically, we investigated (1) phylogenetic relationships among genera in the subtribe, (2) the congruence between previous classifications of the subtribe and the phylogenetic relationships inferred from the molecular data, and (3) evolutionary trends of taxonomically important characters of the subtribe, such as pollinia, a spurred lip, and a column foot. In all, 75 species representing 62 genera in subtribe Aeridinae were examined. Our analyses provided the following insights: (1) monophyly of subtribe Aeridinae was tentatively supported in which 14 subclades reflecting phylogenetic relationships can be recognized, (2) results are inconsistent with previous classifications of the subtribe, and (3) repeated evolution of previously emphasized characters such as pollinia number and apertures, length of spur, and column foot was confirmed. It was found that the inconsistencies are mainly caused by homoplasy of these characters. At the genus level, Phalaenopsis, Cleisostoma, and Sarcochilus are shown to be non-monophyletic.

Ophioglossella (Orchidaceae-Aeridinae), a New Genus from Papua New Guinea

In the highlands of Papua New Guinea an evidently undescribed orchid belonging to subtribe Aeridinae has been found on several occasions in widely scattered localities, but almost always, it seems, in very low numbers. The scarce material in herbaria (four out of the five available collections are unicates) was identified as Sarcochilus, Pteroceras, Dryadorchis or Grosourdya. Two of these genera (Pteroceras and Grosourdya) are not known to occur in New Guinea, and the New Guinea members of Sarcochilus probably constitute a separate genus. The specimens we have seen are rather variable in the size and shape of the leaves, but they agree in the unusually complex morphology of the labellum. Our attempts to find a genus in which this strange orchid could be accommodated failed, and we concluded (at first independently) that it belonged to an as yet undescribed genus. This so far monotypic genus, which we propose to call Ophioglossella, does show similarities with each of the four genera mentioned above. These in turn belong to a larger group of genera within subtribe Aeridinae that are distinguished by having a mobile labellum, hinged with the apex of a distinct column-foot. Most genera in this group are small, distinctive, and unlikely to be confused with Ophioglossella. A key to those genera with which a closer comparison is justified is provided below.