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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: closed (15 August 2024) | Viewed by 11625

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Prof. Dr. Wen‑Chieh Tsai

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

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Research

16 pages, 10835 KiB

Open AccessArticle

Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence

by Meng-Yao Zeng, Ming-He Li, Siren Lan, Wei-Lun Yin and Zhong-Jian Liu

Int. J. Mol. Sci. 2024, 25(20), 11181; https://doi.org/10.3390/ijms252011181 - 17 Oct 2024

Viewed by 595

Abstract

Malaxidinae is one of the most confusing groups in the Orchidaceae classification. Previous phylogenetic analyses have revealed that the relationships between the taxa in Malaxidinae have not yet been reliably established, using only a few plastome regions and nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a dataset of 19 plastomes, including 17 species of Malaxidinae. The plastome features and phylogenetic relationships were compared and analyzed. The results showed the following: (1) Malaxidinae species plastomes possess the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized to varying degrees in six species. An unusual inversion was detected in the large single-copy region (LSC) of Oberonioides microtatantha. (2) Eight regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trnF^GAA-ndhJ, and trnS^GCU-trnG^UCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes, and 51 intergenic regions, respectively, our phylogenetic analyses revealed the genus-level relationships in this subtribe with strong support. The Liparis was supported as non-monophyletic. Full article

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

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12 pages, 7601 KiB

Open AccessArticle

Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)

by Wanshun Lei, Peng Zhou, Zelong Pei, Yizhen Liu, Yan Luo and Xiaoguo Xiang

Int. J. Mol. Sci. 2024, 25(17), 9538; https://doi.org/10.3390/ijms25179538 - 2 Sep 2024

Viewed by 563

Abstract

Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded Vanda including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of Vanda s.l. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their ndh genes underwent loss or pseudogenization. Comparative plastome analyses of 13 Vanda species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from trnG^GCC to ycf3 in V. coerulea. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that Vanda s.l. is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages. Full article

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

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13 pages, 5766 KiB

Open AccessArticle

The Complete Mitogenome of Apostasia fujianica Y.Li & S.Lan and Comparative Analysis of Mitogenomes across Orchidaceae

by Qinyao Zheng, Xiaoting Luo, Ye Huang, Shi-Jie Ke and Zhong-Jian Liu

Int. J. Mol. Sci. 2024, 25(15), 8151; https://doi.org/10.3390/ijms25158151 - 26 Jul 2024

Viewed by 737

Abstract

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. Full article

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

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16 pages, 5975 KiB

Open AccessArticle

Genome-Based Identification of the Dof Gene Family in Three Cymbidium Species and Their Responses to Heat Stress in Cymbidium goeringii

by Xin He, Meng-Meng Zhang, Ye Huang, Jiali Yu, Xuewei Zhao, Qinyao Zheng, Zhong-Jian Liu and Siren Lan

Int. J. Mol. Sci. 2024, 25(14), 7662; https://doi.org/10.3390/ijms25147662 - 12 Jul 2024

Cited by 1 | Viewed by 915

Abstract

As an important genus in Orchidaceae, Cymbidium has rich ecological diversity and significant economic value. DNA binding with one zinc finger (Dof) proteins are pivotal plant-specific transcription factors that play crucial roles in the growth, development, and stress response of plants. Although the Dof genes have been identified and functionally analyzed in numerous plants, exploration in Orchidaceae remains limited. We conducted a thorough analysis of the Dof gene family in Cymbidium goeringii, C. ensifolium, and C. sinensis. In total, 91 Dof genes (27 CgDofs, 34 CeDofs, 30 CsDofs) were identified, and Dof genes were divided into five groups (I–V) based on phylogenetic analysis. All Dof proteins have motif 1 and motif 2 conserved domains and over half of the genes contained introns. Chromosomal localization and collinearity analysis of Dof genes revealed their evolutionary relationships and potential gene duplication events. Analysis of cis-elements in CgDofs, CeDofs, and CsDofs promoters showed that light-responsive cis-elements were the most common, followed by hormone-responsive elements, plant growth-related elements, and abiotic stress response elements. Dof proteins in three Cymbidium species primarily exhibit a random coil structure, while homology modeling exhibited significant similarity. In addition, RT-qPCR analysis showed that the expression levels of nine CgDofs changed greatly under heat stress. CgDof03, CgDof22, CgDof27, CgDof08, and CgDof23 showed varying degrees of upregulation. Most upregulated genes under heat stress belong to group I, indicating that the Dof genes in group I have great potential for high-temperature resistance. In conclusion, our study systematically demonstrated the molecular characteristics of Dof genes in different Cymbidium species, preliminarily revealed the patterns of heat stress, and provided a reference for further exploration of stress breeding in orchids. Full article

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

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16 pages, 30017 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the GRAS Gene Family and Their Responses to Heat Stress in Cymbidium goeringii

by Ye Huang, Qinyao Zheng, Meng-Meng Zhang, Xin He, Xuewei Zhao, Linying Wang, Siren Lan and Zhong-Jian Liu

Int. J. Mol. Sci. 2024, 25(12), 6363; https://doi.org/10.3390/ijms25126363 - 8 Jun 2024

Cited by 1 | Viewed by 997

Abstract

The GRAS gene family, responsible for encoding transcription factors, serves pivotal functions in plant development, growth, and responses to stress. The exploration of the GRAS gene family within the Orchidaceae has been comparatively limited, despite its identification and functional description in various plant species. This study aimed to conduct a thorough examination of the GRAS gene family in Cymbidum goeringii, focusing on its physicochemical attributes, phylogenetic associations, gene structure, cis-acting elements, and expression profiles under heat stress. The results show that a total of 54 CgGRASs were pinpointed from the genome repository and categorized into ten subfamilies via phylogenetic associations. Assessment of gene sequence and structure disclosed the prevalent existence of the VHIID domain in most CgGRASs, with around 57.41% (31/54) CgGRASs lacking introns. The Ka/Ks ratios of all CgGRASs were below one, indicating purifying selection across all CgGRASs. Examination of cis-acting elements unveiled the presence of numerous elements linked to light response, plant hormone signaling, and stress responsiveness. Furthermore, CgGRAS5 contained the highest quantity of cis-acting elements linked to stress response. Experimental results from RT-qPCR demonstrated notable variations in the expression levels of eight CgGRASs after heat stress conditions, particularly within the LAS, HAM, and SCL4/7 subfamilies. In conclusion, this study revealed the expression pattern of CgGRASs under heat stress, providing reference for further exploration into the roles of CgGRAS transcription factors in stress adaptation. Full article

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

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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

Cited by 1 | Viewed by 1020

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

Cited by 3 | Viewed by 1294

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

Cited by 1 | Viewed by 1412

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

Cited by 4 | Viewed by 1833

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

Cited by 2 | Viewed by 1490

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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