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Molecular Research on Orchid Plants
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Molecular Research on Orchid Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 15 August 2024 | Viewed by 2761

Special Issue Editor

Prof. Dr. Wen‑Chieh Tsai

E-Mail Website
Guest Editor
Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
Interests: plant evolutionary development; genomics; molecular biology

Special Issue Information

Dear Colleague，

Constituting approximately 10% of flowering plant species, orchids display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. A comparison of orchid genomes could improve our understanding of their origins. Diversity and specialization in orchid floral morphology have fascinated botanists for centuries. The complex flower organization of orchids offers an opportunity to discover new variant genes and different levels of complexity in the morphogenesis of flowers. Orchids have been used as a source of medicine to treat different diseases, including tuberculosis, tumour, and inflammation. Some novel compounds and drugs, both in phytochemical and pharmacological points of view, have been reported from orchids. The secondary metabolites present in medicinal orchids possess a vast array of biological activities. Discovering the medical value of novel components in orchid plants is critical.

This Special Issue aims to provide a platform for molecular mechanistic research on orchids, with a special focus on exploring the orchid genomes with genomics tools, the molecular development  of orchid floral morphogenesis, and medicinal properties. We warmly welcome your submission of original papers and reviews based on results from molecular viewpoints.

This Special Issue is supervised by Prof. Dr. Wen‑Chieh Tsai and assisted by our Topical Advisory Panel Member Dr. Shijiang Cao (College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China).

Prof. Dr. Wen‑Chieh Tsai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • orchid
  • genomics
  • genome
  • genes
  • tumor
  • inflammation
  • drug
  • transcriptomics

Published Papers (3 papers)

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17 pages, 6892 KiB  
Article
Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in Cymbidium sinense
by Linying Wang, Xuewei Zhao, Ruiyue Zheng, Ye Huang, Cuili Zhang, Meng-Meng Zhang, Siren Lan and Zhong-Jian Liu
Int. J. Mol. Sci. 2024, 25(5), 3031; https://doi.org/10.3390/ijms25053031 - 06 Mar 2024
Viewed by 600
Abstract
Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism [...] Read more.
Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism of the NF-Y gene family’s response to abiotic stress in orchids has not yet been reported. In this study, phylogenetic analysis allowed for 27 CsNF-Y genes to be identified (5 CsNF-YAs, 9 CsNF-YBs, and 13 CsNF-YC subunits), and the CsNF-Ys were homologous to those in Arabidopsis and Oryza. Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. Secondary and tertiary protein structure analysis indicated that the CsNF-YB and CsNF-YC subfamilies had a high content of alpha helix structures. Cis-element analysis showed that elements related to drought stress were mainly concentrated in the CsNF-YB and CsNF-YC subfamilies, with CsNF-YB3 and CsNF-YC12 having the highest content. The results of a transcriptome analysis showed that there was a trend of downregulation of almost all CsNF-Ys in leaves under drought stress, while in roots, most members of the CsNF-YB subfamily showed a trend of upregulation. Additionally, seven genes were selected for real-time reverse transcription quantitative PCR (qRT-PCR) experiments. The results were generally consistent with those of the transcriptome analysis. The regulatory roles of CsNF-YB 1, 2, and 4 were particularly evident in the roots. The findings of our study may make a great contribution to the understanding of the role of CsNF-Ys in stress-related metabolic processes. Full article
(This article belongs to the Special Issue Molecular Research on Orchid Plants)
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19 pages, 6198 KiB  
Article
The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis
by Yuwei Wu, Meng-Yao Zeng, Huan-Xin Wang, Siren Lan, Zhong-Jian Liu, Shibao Zhang, Ming-He Li and Yunxiao Guan
Int. J. Mol. Sci. 2024, 25(5), 2665; https://doi.org/10.3390/ijms25052665 - 25 Feb 2024
Viewed by 854
Abstract
Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations [...] Read more.
Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we report the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste, and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and a GC content of 36.60% to 38.04%. Each genome contained 125–132 genes, encompassing 74–86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents, and length were similar, with differences observed in ndh gene composition. It is worth noting that there were exogenous fragment insertions in the IR regions of B. crassipes. A total of 18–49 long repeats and 38–80 simple sequence repeats (SSRs) were detected and the single nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed that leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions (rpl32-trnLUAG > trnTUGU-trnLUAA > trnFGAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnSGCU) and five coding sequences (ycf1 > rps12 > matK > psbK > rps15) were identified as potential DNA markers based on nucleotide diversity. Additionally, 31,641 molecular diagnostic characters (MDCs) were identified in complete cp genomes. A phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported that 28 Bulbophyllum species can be divided into four branches, sects. Brachyantha, Cirrhopetalum, and Leopardinae, defined by morphology, were non-monophyly. Our results enriched the genetic resources of Bulbophyllum, providing valuable information to illustrate the complicated taxonomy, phylogeny, and evolution process of the genus. Full article
(This article belongs to the Special Issue Molecular Research on Orchid Plants)
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14 pages, 10342 KiB  
Article
Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids
by Zhuang Zhao, Yuanyuan Li, Jun-Wen Zhai, Zhong-Jian Liu and Ming-He Li
Int. J. Mol. Sci. 2024, 25(3), 1578; https://doi.org/10.3390/ijms25031578 - 27 Jan 2024
Viewed by 891
Abstract
Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled [...] Read more.
Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants. Full article
(This article belongs to the Special Issue Molecular Research on Orchid Plants)
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