Orchid Research Articles

Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

BackgroundHabenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.ResultsWe sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259–155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.ConclusionsThe results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.

Exploring the medicinal potential of Dendrobium: Uncovering the spatial distribution of flavonoids and alkaloids in 15 species of Dendrobium using MALDI-MSI

Dendrobium, the second largest genus in the Orchidaceae family, has been regarded as a valuable medicinal plant throughout Chinese history. Secondary metabolites present in the stem of Dendrobium, including alkaloids and flavonoids, confer significant pharmacological effects such as anti-inflammatory, antibacterial, immunomodulatory, antitumor, and antioxidant properties. To our knowledge, this study is the first to apply matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technology to comprehensively identify the spatial distribution of secondary metabolites, particularly flavonoids and alkaloids, in the mature stems of 15 common Dendrobium species. By analyzing the matching scores and relative concentrations of compounds, 20 flavonoids and 19 alkaloids with high identification credibility were identified, along with 4 sesquiterpenoid compounds. Their spatial distributions and compositions were analyzed, and the results revealed that despite the similar structural basis of the stems in the 15 Dendrobium species, significant differences existed in the distribution of secondary metabolites among different species. Flavonoids and alkaloids with different medicinal effects exhibited certain specific distribution patterns; for instance, flavonoids with antioxidant effects were mostly concentrated in the outer circle of thin-walled cells of Dendrobium stems, whereas those with antitumor effects were found in higher concentrations in the central areas of some Dendrobium species than in the periphery. Alkaloids with antitumor properties typically exhibited a higher concentration in peripheral thin-walled cells than in central regions. Furthermore, statistical analysis was conducted on the content of secondary metabolites with different effects among the 15 Dendrobium species to identify species with greater medicinal potential in terms of antioxidant and antitumor effects. The findings of this study not only enhance our understanding of the distribution patterns of flavonoids and alkaloids within Dendrobium stems but also offer valuable insights for the medicinal development and quality assessment of Dendrobium.

Pollinator diversity of the food-deceptive orchids in southern Italy.

The orchid family is renowned for its enormous diversity in pollination biology. Many orchid species use deception to attract pollinators, and the main strategy in terrestrial orchids is food deception. Food-deceptive orchids usually show a low number of pollinator visitations, making field observations of pollinators difficult. In this study visual census, pollinator capture and molecular analysis of pollinaria found on caught insects allowed us to obtain information on species composition of orchid pollinators. A total of 321 insects were caught; most specimens were hymenopterans (Apis mellifera, Bombus ruderatus and Eucera rufa) and coleopterans (Tropinota hirta and T. squalida). The identity of species to which pollinaria found on the insect's body belonged was confirmed by molecular analysis. Moreover, some individuals of Billaea lata (Tachinidae, Diptera) were captured and photographed with the pollinaria on their head. Two new and important results emerged clearly in this work: a dipteran, Billaea lata, pollinator of Anacamptis pyramidalis, and two beetles in the genus Tropinota are pollinators of Orchis italica. Our results confirm that generalized food-deceptive orchids of the genera Orchis and Anacamptis show weak pollinator specificity.

Properties Characterization and Identification of Saponarin and Ribosnarin (apigenin-6-C-ribosyl -7-O-glucoside) Extracted Abundantly from the White-Color Moth Orchid Flowers (Phalaenopsis Hybrids)

Properties Characterization and Identification of Saponarin and Ribosnarin (apigenin-6-C-ribosyl -7-O-glucoside) Extracted Abundantly from the White-Color Moth Orchid Flowers (Phalaenopsis Hybrids)

Specialized seed dispersal in Neotropical Vanilla reveals fruit unpalatability to omnivores.

Flowering plants are essentially sessile organisms that disperse their genes through pollination, expanding their areas of occurrence through seed dispersal. In orchids, seed dispersal is commonly mediated by air currents. Conversely, members of several genera have evolved seeds adapted to endozoochory. This is the case for Vanilla, the most economically important genus in the orchid family. The role of indehiscent fruits in the attraction and rewarding of Vanilla seed dispersers was investigated based on field observations, analysis of fragrances, reward substances, and investigation of seed viability through the digestive tract. Indehiscent Vanilla fruits are consumed exclusively by herbivores, i.e. agoutis. Besides providing nutritional rewards, the fruits are rich in polyphenols that are unpalatable to omnivores. The most dominant compound in fruits is attractive only to agoutis. This is the first study showing synzoochory in Orchidaceae and specificity of seed dispersal in orchids. Indehiscent fruits may have evolved early in Neotropical Vanilla in response to selection pressures mediated by large herbivores as the genus emerged ca. 34 Mya in South America, concomitantly with megafauna diversification in the Oligocene. Extinction of the megafauna during the Pleistocene has left agoutis as inheritors of seed dispersal in species with large fleshy fruits. Apart from the effects on omnivores, this study shows that indehiscent fruits of V. chamissonis are consumed exclusively by agoutis, providing the first evidence of target mutualism in orchid seed dispersal.

Flowers meet Newton: testing the role of gravitational pull in resupination of orchid flowers.

Resupination refers to the developmental orientation changes of flowers through ≈180º, leaving them effectively upside-down. It is a widespread trait present in 14 angiosperm families, including the Orchidaceae, where it is a gravitropic phenomenon actively controlled by auxins. Here, we demonstrate that the passive gravitational pull on flower parts can have an additional influence on resupination. We studied a lady's slipper orchid in which some flowers naturally fail to resupinate. We conducted a manipulative experiment removing floral parts and showed that both the probability of complete resupination and the degree of flower vertical movement (from 0º - 180º) are related to the mass of floral organs. During flower development, the tip of the ovary slightly curves actively (14.75º) due to gravitropism. This promotes a lever arm effect so that the gravitational pull acting on flower mass creates a torque that bends the ovary, orienting the flower into a resupinate position that is accessible to pollinators. The role of the mass of floral organs in resupination provides new insights into flower development and its role in pollination mechanisms.

Characterization of the complete chloroplast genome of Liparis gigantea (Orchidaceae)

Liparis gigantea is a Chinese traditional medicinal herb in the Orchidaceae family. It is a rare and special Liparis species that exhibits relatively large flowers. To illuminate its phylogenetic status and augment genomic resources, the complete chloroplast (cp) genome of L. gigantea was first sequenced and assembled using whole genome next-generation sequencing in this study. The cp genome size is 158,462 bp with a total GC content of 36.9%. Characterized by a quadripartite structure, the genome consists of a large single-copy (LSC) region of 86,032 bp, a small single-copy (SSC) region of 18,322 bp, which is separated by a pair of 27,054 bp inverted repeat regions (IRs). A total of 133 genes were annotated, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis strongly supported L. gigantea as the sister to two closely related terrestrial species, Liparis nervosa and L. vivipara. The results of this study provide genomic information for future research and application of this medicinal herb.

Chemistry and Biotechnological Insights of Rhynchostylis retusa (L.) Blume: A Mini-Review

Abstract: Rhynchostylis retusa (L.) Blume belongs to the Vanda alliance of the Orchidaceae family and is mostly distributed from 300-1,500 m. It is traditionally practiced for the treatment of health issues such as dysentery, pain, inflammation, arthritis, and, skin, respiratory, heart, kidney, brain, and menstrual problems. R. retusa is also used in folklore claims to recover from tuberculosis, vertigo, anemia, and bone fractures. Further, some of the traditional claims were scientifically validated through preclinical (In vitro & in vivo) studies. With the view of tremendous health benefits, the current study was focused on harnessing the information through search engines (Google Scholar, Scopus-Elsevier, Medline, Sci Finder, Web of Science, Plant list, and Directory of Open Access Journal) till October 2022 and compile them as a comprehensive review. Therefore, detailed, comprehensive information on botanical distribution, ethnopharmacological and ornamental values, chemistry, biotechnological interventions for smart cultivation, pharmacological activities, conservation status, patents, and future perspectives of the R. retusa has been compiled. The comprehensive review of the Foxtail Orchid (R. retusa) has unremarkable potential and still needs to be explored from chemical, pharmacological, quality control, and value addition perspectives. The review will help the orchid community as well as researchers and farmers working on orchids.

Time to flowering of ornamental orchids

Objective: To analyze features of time to flowering of orchids and some strategies for its control in cultivation for ornamental purposes. Design/methodology/approach: Information from various authors and our own data is shown, in relation to the management of flowering time of ornamental orchids, based on treatments of environmental effects, plant growth regulators (PGRs) and nutrition. Findings/conclusions: It is possible to reduce the flowering time of orchids by environmental modifications, mainly temperature and photoperiod. This can also be achieved by nutritional management, mainly macro-nutritional, and through organic nutrition and PGRs. However, much more information is needed, especially for native orchid species with ornamental potential.

Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae.

The yellow-flowered Spathoglottis aurea (tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship between S. aurea and the geographically isolated S. microchilina from Borneo that has encouraged further study of the S. aurea populations, but the genomic resource for S. aurea has not yet been reported. The present study reports the first work to characterize a chloroplast (cp) genome among the Spathoglottis genus. The complete cp genome of S. aurea was assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome of S. aurea is 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite cp genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of the S. aurea cp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed that S. aurea has a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such as Phaius and Cephalantheropsis.

Pollination ecology of Dracula erythrochaete (Orchidaceae): brood-site imitation or food deception?

Abstract Pleurothallidinae is the most diverse Neotropical subtribe in Orchidaceae and is almost exclusively pollinated by insects of the order Diptera. Dracula, a genus of 138 species in the Pleurothallidinae, is known to attract Zygothrica (Drosophilidae) flies, common macrofungi visitors, by imitating fungal volatile compounds and lamellae. Interestingly, Dracula orchids do not appear to offer any rewards to their floral visitors. While brood-site imitation of macrofungi has been suggested as their pollination system, the exact behaviour of flies during their extended visits to the orchid flowers has yet to be confirmed. In this study, we document the pollination mechanism of Dracula erythrochaete. We characterize the floral structures involved in the mechanism using anatomical and morphological evidence. Additionally, through in situ observations and camera recordings, we describe the insect behaviour. We show that flowers of D. erythrochaete share the same group of visitors as nearby macrofungi, including different Zygothrica species, seven of which were determined as effective pollinators. Male and female flies were attracted to the flowers and displayed feeding behaviour. Accordingly, proteins were detected in high concentrations on the papillae at the base of the movable lip and in papillary trichomes of the sepals, near the column. The concept of brood-site imitation is debated, as no oviposition events were observed and no eggs were found on the flowers. Therefore, a mixed strategy of congregation/brood-site imitation and food reward is proposed for pollination.

Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae).

In order to understand the bias and main affecting factors of codon usage in the plastid genome of Diplandrorchis sinica, which is a rare and endangered plant species in the Orchidaceae family, the complete plastid genome sequence of D. sinica was downloaded from the GenBank database and 20 protein-coding sequences that met the analysis requirements were finally selected. The GC content, length of the amino acid (Laa), relative synonymous codon usage (RSCU), and effective number of codon (ENC) of each gene and codon were calculated using the CodonW and EMBOSS online programs. Neutral plot analysis, ENC-plot analysis, PR2-plot analysis, and correspondence analysis were performed using Origin Pro 2024 software, and correlation analysis between various indicators was performed using SPSS 23.0 software. The results showed that the third base of the codon in the plastid genome of D. sinica was rich in A and T, with a GC3 content of 27%, which was lower than that of GC1 (45%) and GC2 (39%). The ENC value ranged from 35 to 57, with an average of 47. The codon usage bias was relatively low, and there was a significant positive correlation between ENC and GC3. There were a total of 32 codons with RSCU values greater than 1, of which 30 ended with either A or U. There were a total of nine optimal codons identified, namely, UCU, UCC, UCA, GCA, UUG, AUA, CGU, CGA, and GGU. This study indicated that the dominant factor affecting codon usage bias in the plastid genome of D. sinica was natural selection pressure, while the impact of base mutations was limited. The codon usage patterns were not closely related to gene types, and the distribution of photosynthetic system genes and ribosomal protein-coding gene loci was relatively scattered, indicating significant differences in the usage patterns of these gene codons. In addition, the codon usage patterns may not be related to whether the plant is a photosynthetic autotrophic or heterotrophic nutritional type. The results of this study could provide scientific references for the genomic evolution and phylogenetic research of plant species in the family Orchidaceae.

Characterization of Flower’s Color based on CHS Gene Structure in <i>Phalaenopsis</i> ‘OX Queen’ and <i>Dendrobium</i> ‘Cheddi Jagan’ Orchids

Orchids (Orchidaceae) are ornamental plants known for their high aesthetic value attributed to the shapes, colours, and fragrances of their flowers. Two types of hybrid orchids with attractive flowers, namely the Phalaenopsis 'OX Queen' orchid and the Dendrobium 'Cheddi Jagan' boast attractive flowers were used in this research, because of the beauty of its flower colour. The objective of this research is to characterise the morphology of flower colour and CHS (Chalcone Synthase) gene content that induces flower colour. The method used in this research analyzing the flower’s colour by using the RHS (Royal Horticultural Society) colour chart and molecular analysis by DNA genomic isolation and PCR amplification of gDNA for CHS gene specific primers. The results showed that purple colour is observed through the RHS, with P. 'OX Queen' coded as Deep Purple Pink (N73A) and D. 'Cheddi Jagan' coded as Strong Reddish Purple (N72C). The CHS gene can be amplified in P. ’OX Queen’ 1,287 bp and D. ’Cheddi jagan’ 3,731 bp. In both orchids, the results of amplification showed CHS motifs with conserved domains PLN03172 and PLN03170. The research results show that there is a significant difference in the morphology of the flowers of orchids. Purple colour is observed through the RHS, with P. 'OX Queen' coded as N73A and D. 'Cheddi Jagan' coded as N73C. The results showed that gDNA can be isolated by using CTAB method according to Murray and Thomson, and the CHS gene can be amplified by using CHS primers, resulting 1200 bp of P. 'OX Queen' and 2500 bp for D. 'Cheddi Jagan'. Through this study, preliminary data is expected to be obtained for future research, which is the formation of variegated flowers through editing the CRISPR/Cas9 genome in the CHS gene. This research is intended to support further studies on the formation of variegated flower patterns in P. 'OX Queen' and D. 'Cheddi Jagan’, focusing on the CHS gene using CRISPR/Cas9 technique.

Clonal propagation of rare orchid species Paphiopedilum spp. (Orchidaceae) to save Indonesian biodiversity

Paphiopedilum spp. is one of the terrestrial orchids that is interesting as an ornamental plant. This orchid flower has a distinctive characteristic, namely its labellum resembles a sac, so it is sought after by ornamental flower collectors because of its uniqueness. This orchid is included in the Appendix I group according to CITES, namely a critical species that is threatened with extinction, so it needs to be conserved both in situ and ex situ. Ex situ conservation can be done by propagating orchids using in vitro culture techniques. The objective of this research is to carry out mass propagation of 3 species of Paphiopedilum spp orchids: P. supardii, P. primulinum, P. glaucophyllum through somatic embryogenesis and to characterize the existence of embryo gene RKD4 homolog in Paphiopedilum orchids. The method is to culture the nodes slices in dark conditions for 2 weeks, and then changed to photoperiod mode 16:8 hours (dark:light) on ½ MS media plus a combination of 2,4-D or NAA with TDZ. The somatic embryo were analyzed anatomically. This method is an improvement over previously reported methods for Paphiopedilum spp. due to its efficiency and reproducibility for conservation. We concluded that ½ MS media with a combination of NAA or 2,4D with TDZ were able to induce somatic embryogenesis. The result show that 3 mg L−1 NAA was the best PGRs for PLBs induction in P. supardii (50 %), 1 mg L−1 2,4-D + 0.5 mg L−1 TDZ was the best PGRs for callus embryogenic induction in P. primulinum (20 %), and 1 mg L−1 NAA was the best PGRs for PLBs induction in P. glaucophyllum (33 %).

Genome-wide identification of Ankyrin (ANK) repeat gene families in three Dendrobium species and the expression of ANK genes in D. officinale under gibberellin and abscisic acid treatments

BackgroundDendrobium Sw. represents one of the most expansive genera within the Orchidaceae family, renowned for its species’ high medicinal and ornamental value. In higher plants, the ankyrin (ANK) repeat protein family is characterized by a unique ANK repeat domain, integral to a plethora of biological functions and biochemical activities. The ANK gene family plays a pivotal role in various plant physiological processes, including stress responses, hormone signaling, and growth. Hence, investigating the ANK gene family and identifying disease-resistance genes in Dendrobium is of paramount importance.ResultsThis research identified 78 ANK genes in Dendrobium officinale Kimura et Migo, 77 in Dendrobium nobile Lindl., and 58 in Dendrobium chrysotoxum Lindl. Subsequently, we conducted comprehensive bioinformatics analyses on these ANK gene families, encompassing gene classification, chromosomal localization, phylogenetic relationships, gene structure and motif characterization, cis-acting regulatory element identification, collinearity assessment, protein-protein interaction network construction, and gene expression profiling. Concurrently, three DoANK genes (DoANK14, DoANK19, and DoANK47) in D. officinale were discerned to indirectly activate the NPR1 transcription factor in the ETI system via SA, thereby modulating the expression of the antibacterial PR gene. Hormonal treatments with GA3 and ABA revealed that 17 and 8 genes were significantly up-regulated, while 4 and 8 genes were significantly down-regulated, respectively. DoANK32 was found to localize to the ArfGAP gene in the endocytosis pathway, impacting vesicle transport and the polar movement of auxin.ConclusionOur findings provide a robust framework for the taxonomic classification, evolutionary analysis, and functional prediction of Dendrobium ANK genes. The three highlighted ANK genes (DoANK14, DoANK19, and DoANK47) from D. officinale may prove valuable in disease resistance and stress response research. DoANK32 is implicated in the morphogenesis and development of D. officinale through its role in vesicular transport and auxin polarity, with subcellular localization studies confirming its presence in the nucleus and cell membrane. ANK genes displaying significant expression changes in response to hormonal treatments could play a crucial role in the hormonal response of D. officinale, potentially inhibiting its growth and development through the modulation of plant hormones such as GA3 and ABA.

Comprehensive Screening and Characterization of α-glucosidase Inhibitory Components in the Edible Medicinal Plant Pholidota cantonensis Rolfe Using UPLC-Q-TOF-MS/MS Analysis and Molecular Docking.

Pholidota cantonensis Rolfe is an edible medicinal plant in the genus Pholidota of the family Orchidaceae. This plant is used to prepare medicated food in China and has been reported to possess anti-α-glucosidase activity. To date, little is known about the active substances responsible for the observed anti-α-glucosidase activity. In the present study, we aimed to screen and characterize the α-glucosidase inhibitory fraction of P. cantonensis using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) analysis and molecular docking. As a result, the 50% ethanol fraction obtained from D101 macroporous adsorption resin column chromatography (D50 fraction) had the highest total phenol content (353.83 ± 6.06mg GAE/g) and the most prominent α-glucosidase inhibitory activity (IC50 = 30.01 ± 7.30µg/mL). Forty-five compounds were identified from the D50 fraction by using UPLC-Q-TOF-MS/MS analysis. Molecular docking results showed that six main constituents, namely, crepidatin, 2,7-dihydroxy-4-methoxyl-9,10-dihydrophenylene, 4,4',5,6-tetrahydroxystilbene, 4,7-dihydroxy-2-methoxyl-9,10-dihydrophenylene, (-)-lariciresinol, and thunalbene, in the D50 fraction occupied the catalytic sites of α-glucosidase through strong hydrophobic interactions, hydrogen bonding, and other patterns. The binding energies were between - 29.95 and - 11.41kJ/mol, indicating good binding between the tested compounds and α-glucosidase. The active ingredients responsible for the α-glucosidase inhibitory activity may include phenanthrenes, stilbenes, dibenzyls, and lignans. The D50 fraction has potential value for developing innovative drugs for the prevention and treatment of diabetes mellitus (DM) and is worthy of in-depth research.

Integrated metabolomic and transcriptomic analysis reveals variation in the metabolites of Dendrobium officinale, Dendrobium huoshanense, Dendrobium nobile.

Dendrobium is a perennial herb of the genus Dendrobium in the orchid family. Generally, Dendrobium officinale (TP) and Dendrobium huoshanense (HS) are both considered to have the function of yin-nourishing, while Dendrobium nobile (JC) has better efficacy of heat-clearing. However, because of the wide variety of Dendrobium species, the classification and clinical application of Dendrobium are often confused clearly distinguished in different medicinal uses. In order to compare the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) of the three Dendrobium. We selected TP, HS, and JC cultivated on stone for metabolomic and transcriptomic analyses between 2 and 3 years. The results showed that a total of 489 metabolites were obtained, including 72 were DAMs. The 72 DAMs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. Transcriptome analysis results showed that 1,038 annotated DEGs were identified among the three Dendrobium species. The comprehensive analysis showed that the three Dendrobium differed in the distribution of the content of four major active components: flavonoids, amino acids, alkaloids, and sugars and alcohols, among which the DAMs and DEGs were mainly enriched in metabolic pathways and secondary metabolite biosynthesis. In this study, metabolomics and transcriptomics were utilized to compare the differences among the three species of Dendrobium, to provide theoretical references for future research and selection of different species of Dendrobium based on different medicinal uses, and to lay the foundation for further research on the biosynthesis of flavonoids in Dendrobium.

An efficient and green strategy for the synthesis of graphene with aqueous polyphenol extracts of orchid flower (Dendrobium Anosmum) for charge storage

This study introduces the use of orchid flower extract as a green reducing agent for the first time to produce reduced graphene oxide (ORGO). Raman, XRD and FTIR confirmed the reduction process whereas TGA analysis provides the thermal stability of the prepared samples. SEM imaging validates the improved morphology of ORGO as compared to the crumpled and folded region of graphene oxide (GO). Electrochemical tests reveal ORGO’s superior specific capacitance (489.8F/g) value at scan rate of 20 mV/s, low charge transfer resistance (2.1 Ω) and high specific capacity retention (96.63 %) after 10,000 cycles, highlighting its potential application for charge storage devices.

Comparative analysis of the mitochondrial genomes of four Dendrobium species (Orchidaceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing.

The genus Dendrobium, part of the Orchidaceae family, encompasses species of significant medicinal, nutritional, and economic value. However, many Dendrobium species are threatened by environmental stresses, low seed germination rates, and overharvesting. Mitochondria generate the energy necessary for various plant life activities. Despite their importance, research on the mitochondrial genomes of Dendrobium species is currently limited. To address this gap, we performed a comprehensive genetic analysis of four Dendrobium species-D. flexicaule, D. nobile, D. officinale, and D. huoshanense-focusing on their mitochondrial and chloroplast genomes to elucidate their genetic architecture and support conservation efforts. We utilized advanced sequencing technologies, including Illumina for high-throughput sequencing and Nanopore for long-read sequencing capabilities. Our findings revealed the multichromosomal mitochondrial genome structures, with total lengths ranging from 596,506 bp to 772,523 bp. The mitochondrial genomes contained 265 functional genes, including 64-69 protein-coding genes, 23-28 tRNA genes, and 3 rRNA genes. We identified 647 simple sequence repeats (SSRs) and 352 tandem repeats, along with 440 instances of plastid-to-mitochondrial gene transfer. Additionally, we predicted 2,023 RNA editing sites within the mitochondrial protein-coding genes, predominantly characterized by cytosine-to-thymine transitions. Comparative analysis of mitochondrial DNA across the species highlighted 25 conserved genes, with evidence of positive selection in five genes: ccmFC, matR, mttB, rps2, and rps10. Phylogenetic assessments suggested a close sister relationship between D. nobile and D. huoshanense, and a similar proximity between D. officinale and D. flexicaule. This comprehensive genomic study provides a critical foundation for further exploration into the genetic mechanisms and biodiversity of Dendrobium species, contributing valuable insights for their conservation and sustainable utilization.

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.