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Molecular Research on Orchid Plants

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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 3770

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Prof. Dr. Wen‑Chieh Tsai

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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

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Keywords

orchid
genomics
genome
genes
tumor
inflammation
drug
transcriptomics

Published Papers (5 papers)

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Research

16 pages, 8031 KiB

Open AccessArticle

Genome-Wide Identification and Expression Pattern Analysis of TIFY Family Genes Reveal Their Potential Roles in Phalaenopsis aphrodite Flower Opening

by Yunxiao Guan, Qiaoyu Zhang, Minghe Li, Junwen Zhai, Shasha Wu, Sagheer Ahmad, Siren Lan, Donghui Peng and Zhong-Jian Liu

Int. J. Mol. Sci. 2024, 25(10), 5422; https://doi.org/10.3390/ijms25105422 - 16 May 2024

Viewed by 224

Abstract

The TIFY gene family (formerly known as the zinc finger proteins expressed in inflorescence meristem (ZIM) family) not only functions in plant defense responses but also are widely involved in regulating plant growth and development. However, the identification and functional analysis of TIFY proteins remain unexplored in Orchidaceae. Here, we identified 19 putative TIFY genes in the Phalaenopsis aphrodite genome. The phylogenetic tree classified them into four subfamilies: 14 members from JAZ, 3 members from ZML, and 1 each from PPD and TIFY. Sequence analysis revealed that all Phalaenopsis TIFY proteins contained a TIFY domain. Exon–intron analysis showed that the intron number and length of Phalaenopsis TIFY genes varied, whereas the same subfamily and subgroup genes had similar exon or intron numbers and distributions. The most abundant cis-elements in the promoter regions of the 19 TIFY genes were associated with light responsiveness, followed by MeJA and ABA, indicating their potential regulation by light and phytohormones. The 13 candidate TIFY genes screened from the transcriptome data exhibited two types of expression trends, suggesting their different roles in cell proliferation and cell expansion of floral organ growth during Phalaenopsis flower opening. Overall, this study serves as a background for investigating the underlying roles of TIFY genes in floral organ growth in Phalaenopsis. Full article

(This article belongs to the Special Issue Molecular Research on Orchid Plants)

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17 pages, 6586 KiB

Open AccessArticle

The Evolution of the WUSCHEL-Related Homeobox Gene Family in Dendrobium Species and Its Role in Sex Organ Development in D. chrysotoxum

by Xiaoting Luo, Qinyao Zheng, Xin He, Xuewei Zhao, Mengmeng Zhang, Ye Huang, Bangping Cai and Zhongjian Liu

Int. J. Mol. Sci. 2024, 25(10), 5352; https://doi.org/10.3390/ijms25105352 - 14 May 2024

Viewed by 372

Abstract

The WUSCHEL-related homeobox (WOX) transcription factor plays a vital role in stem cell maintenance and organ morphogenesis, which are essential processes for plant growth and development. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are valued for their ornamental and medicinal properties. However, the specific functions of the WOX gene family in Dendrobium species are not well understood. In our study, a total of 30 WOX genes were present in the genomes of the three Dendrobium species (nine DchWOXs, 11 DhuWOXs, and ten DnoWOXs). These 30 WOXs were clustered into ancient clades, intermediate clades, and WUS/modern clades. All 30 WOXs contained a conserved homeodomain, and the conserved motifs and gene structures were similar among WOXs belonging to the same branch. D. chrysotoxum and D. huoshanense had one pair of fragment duplication genes and one pair of tandem duplication genes, respectively; D. nobile had two pairs of fragment duplication genes. The cis-acting regulatory elements (CREs) in the WOX promoter region were mainly enriched in the light response, stress response, and plant growth and development regulation. The expression pattern and RT-qPCR analysis revealed that the WOXs were involved in regulating the floral organ development of D. chrysotoxum. Among them, the high expression of DchWOX3 suggests that it might be involved in controlling lip development, whereas DchWOX5 might be involved in controlling ovary development. In conclusion, this work lays the groundwork for an in-depth investigation into the functions of WOX genes and their regulatory role in Dendrobium species’ floral organ development. Full article

(This article belongs to the Special Issue Molecular Research on Orchid Plants)

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17 pages, 6892 KiB

Open AccessArticle

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 - 6 Mar 2024

Viewed by 715

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 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

Open AccessArticle

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 986

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 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-trnL^UAG > trnT^UGU-trnL^UAA > trnF^GAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnS^GCU) 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

Open AccessArticle

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 982

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 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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