Phylogenetic relationships of the orchid genus Spathoglottis (Orchidaceae: Collabieae) in Peninsular Malaysia and Borneo were inferred using the internal transcribed spacer of a nuclear ribosomal DNA (nrITS), a plastid gene maturaseK (matK) and the plastid region trnL-F. Eleven species and three infraspecific taxa of Spathoglottis were examined, with two outgroup species, were included in the phylogenetic analysis. The combined plastid and nuclear data revealed Spathoglottis as monophyletic. From the maximum likelihood, maximum parsimony and Bayesian analyses, Spathoglottis is divided into four major groups which are, (1) the Dwarf Purple Spathoglottis, (2) the Dwarf Yellow Spathoglottis, (3) the Large Purple Spathoglottis, and (4) the Large Yellow Spathoglottis. The split in the Dwarf and Large Spathoglottis groups might reflect an early differentiation of plant size, flower colours and flower size. Phylogeny reconstruction of the orchid genus Spathoglottis also exhibited strong support towards the taxonomic delimitation of the two mostly debated taxa in the genus, S. aurea and S. microchilina.

Analysis of morphological characters and conservation status were carried out for Hymenorchis javanica from Peninsular Malaysia. Morphology was studied in detail and accompanied by a botanical drawing prior to the correct identification. From most closely related Hymenorchis phitamii found in Vietnam, it differs in the lip ovate-oblong with apex acute and margins entire, and the leaves margins prominently serrulate. Based on the current IUCN criteria, we proposed H. javanica as an endangered species under the threatened category. Judging from the current small population sizes and degraded habitats, H. javanica in Malaysia is threatened by extinction in the wild.

Jasim JHM, Othman AS, Nordin FA, Talkah NSM. 2024. High-quality genomic DNA extraction methods of Yellow Spathoglottis Blume complex for next-generation sequencing. Biodiversitas 25: 654-663. Advancements in genomic research have spurred a growing interest in extracting high-quality genomic DNA, particularly from intricate plant species like the Yellow Spathoglottis Blume Complex. The preparation of genomic DNA high-quality from a plant sample is a crucial step for genomic and genetic analysis studies. A variety of genomic DNA extraction methods such as the traditional Hexadecyltrimethylammonium Bromide (CTAB) method and commercially available kits have been reported. Even so, they are either low purity and yield or costly. We develop a good-quality genomic DNA extraction method from fresh and dried leaves of the Yellow Spathoglottis Blume complex in Peninsular Malaysia, specifically tailored for Next-Generation Sequencing (NGS) applications. Three DNA extraction methods were compared traditional CTAB, modified CTAB, and the DNeasy Qiagen plant mini kit methods. The yield and quality of extracted DNA were assessed by PCR amplification using nuclear ETS and ITS genes performed to evaluate the success of DNA extraction. Additionally, the suitability of the modified CTAB method for NGS library preparation and sequencing was tested. It demonstrated better PCR amplification results, yielding high-concentration bands for both ETS and ITS primers. Furthermore, the modified CTAB method proved suitable for high molecular weight DNA extraction, without contamination. The extracted DNA from Spathoglottis aurea exhibited high molecular weight and passed the quality control assessment for NGS library preparation. Sequencing results demonstrated an average quality score of 36.0, with an accurate base call rate of approximately 99.9%. The developed method enables reliable genomic analysis and sequencing of the Yellow Spathoglottis Blume complex, contributing to further research and understanding of this species group.

Seventy-two morphological characters and three ecological characteristics were measured to assess variation and phylogenetic relationships among twelve species and three infraspecific taxa of the genus Spathoglottis from Peninsular Malaysia and Borneo. The morphological analyses divided Spathoglottis into two main groups based on the colours of the flower: Purple-Flowered Spathoglottis and Yellow-Flowered Spathoglottis. Species within the two groupings were further classified based on the size of the plants (Large/Dwarf Purple Spathoglottis and Large/Dwarf Yellow Spathoglottis) and the shapes of the labellum (spathulate, bilobulate or narrow/thread–like). The selected morphological characters appeared to support the taxonomic boundaries between two mostly debated taxa in the genus, S. aurea and S. microchilina.

To date, documentation of the diversity of orchids from the limestone hills in the northern part of Peninsular Malaysia, particularly in the states of Kedah and Perak, is still lacking, with limited literature available. There is indeed an urgent need to fill this knowledge gap, so that proper documentation of the diversity of orchids from this unique karst habitat can be prepared. In this study, a series of 12 months of diversity assessments on five limestone hills in Kedah and Perak has resulted in the discovery of 56 orchid species from 37 genera. From this account, 12 species are new records within Kedah and 2 species are new records within Malaysia, namely Bulbophyllum meson J.J.Verm., Schuit. & de Vogel and Luisia brachystachys (Lindl.) Blume. Three species are endemic to Peninsular Malaysia which are Anoectochilus sanguineus P.T.Ong & P.O’Byrne, Cheirostylis goldschmidtiana Schltr. and Phalaenopsis appendiculata Carr. Findings of two keystone species, the long-lost Cheirostylis goldschmidtiana and the endangered snow-white slipper orchid, Paphiopedilum niveum (Rchb.f.) Stein, have catalyzed the need for a more comprehensive study to unveil the species richness and endemism within a limestone habitat. Heat maps using geographical data produced from ArcGIS software have enabled precise determination of the areas with the highest concentration of orchid diversity. Results from this study have shown that Gunung Fakir Terbang houses the greatest number of orchid species, followed by Gunung Batu Putih and Gunung Baling. Meanwhile, lower species occurrences were recorded from Gunung Pulai and Gunung Pong. However, lack of attention and delayed conservation action on this unique karst habitat would only lead to more habitat loss, leading to the decline of limestone orchid populations. Orchids as well as other plants are threatened by anthropogenic activity such as quarrying and forest clearing for agriculture. Thus, the results of this study will serve as baseline data for future work in documenting and conserving limestone orchids and their karst habitat in northern Peninsular Malaysia.

A comprehensive assessment on the orchid flora of Gunung Ledang, Johor, Malaysia was carried out from 2012 to 2018 with the aim to re-evaluate the presence of orchid species listed by Ridley in his “Journal of the Straits Branch of the Royal Asiatic Society 35:1–28”, published in 1901, after more than 100 years. The relevant account for comparison is also listed, noting that Ridley’s historical collections were for the isolated group of hills commonly known as Gunung Ledang (Mount Ophir), while the collated item in Orchidaceae is part of catalogues for the whole of Peninsular Malaysia. After Ridley, no account on the orchid flora of Gunung Ledang has been properly given, particularly from the uppermost peak of the mountain, where many interesting plants and orchids are to be found there. This study identified 26 species or 67% were the same as those recorded by Ridley (1901), and 65 species or 83% of Turner (1995) checklist of 270 species of orchids for the state of Malacca and Johor, including the common and widespread species to Peninsular Malaysia. By contribution, this paper provides an updated account on the diversity of orchids in Gunung Ledang, listing 122 species of orchids, of which eight are endemic to Peninsular Malaysia, two are hyper-endemic known only from Gunung Ledang, and 30 were recognised as new records. A comparison table of the current findings against Ridley (1901) and Turner (1995) is provided which shows only 16 species were the same in all three studies.