Transcriptome analysis reveals the key pathways and candidate genes involved in salt stress responses in Cymbidium ensifolium leaves

Li, Xiang; Liu, Lanlan; Sun, Shixian; Li, Yanmei; Jia, Lu; Ye, Shili; Yu, Yanxuan; Dossa, Komivi; Luan, Yunpeng

doi:10.1186/s12870-023-04050-z

Cited by 3 publications

(2 citation statements)

References 106 publications

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“…Fujian Province, the origin of C. ensifolium, has experienced dramatic temperature changes and frequent heat events in recent decades [10]. Due to various abiotic stresses, the habitats of C. ensifolium are declining, leading to the shrinking of wild populations [11,12]. C. ensifolium, currently domesticated as vital ornamental orchids, has formed a global industry chain, requiring large quantities to meet market demands.…”

Section: Introductionmentioning

confidence: 99%

General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature

Zheng,

Chen,

Peng

et al. 2024

IJMS

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Heat shock factors (HSFs) are the key regulators of heat stress responses and play pivotal roles in tissue development and the temperature-induced regulation of secondary metabolites. In order to elucidate the roles of HSFs in Cymbidium ensifolium, we conducted a genome-wide identification of CeHSF genes and predicted their functions based on their structural features and splicing patterns. Our results revealed 22 HSF family members, with each gene containing more than one intron. According to phylogenetic analysis, 59.1% of HSFs were grouped into the A subfamily, while subfamily HSFC contained only two HSFs. And the HSF gene families were differentiated evolutionarily between plant species. Two tandem repeats were found on Chr02, and two segmental duplication pairs were observed on Chr12, Chr17, and Chr19; this provided evidence for whole-genome duplication (WGD) events in C. ensifolium. The core region of the promoter in most CeHSF genes contained cis-acting elements such as AP2/ERF and bHLH, which were associated with plant growth, development, and stress responses. Except for CeHSF11, 14, and 19, each of the remaining CeHSFs contained at least one miRNA binding site. This included binding sites for miR156, miR393, and miR319, which were responsive to temperature and other stresses. The HSF gene family exhibited significant tissue specificity in both vegetative and floral organs of C. ensifolium. CeHSF13 and CeHSF15 showed relatively significant expression in flowers compared to other genes. During flower development, CeHSF15 exhibited markedly elevated expression in the early stages of flower opening, implicating critical regulatory functions in organ development and floral scent-related regulations. During the poikilothermic treatment, CeHSF14 was upregulated over 200-fold after 6 h of heat treatment. CeHSF13 and CeHSF14 showed the highest expression at 6 h of low temperature, while the expression of CeHSF15 and CeHSF21 continuously decreased at a low temperature. The expression patterns of CeHSFs further confirmed their role in responding to temperature stress. Our study may help reveal the important roles of HSFs in plant development and metabolic regulation and show insight for the further molecular design breeding of C. ensifolium.

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Section: Introductionmentioning

confidence: 99%

General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature

Zheng,

Chen,

Peng

et al. 2024

IJMS

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“…Cymbidium ensifolium spp., a member of the Orchidaceae and genus Cymbidium, is an ornamental plant known for its vibrant colors, upright stature, and delightful fragrance, which holds high ornamental and economic value [1,2]. In recent years, the expansion of cultivation areas and various external factors, including biotic and abiotic stresses, have greatly impacted its cultivation.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Nucleotide-Binding Site–Leucine-Rich Repeat Gene Family in Cymbidium ensifolium and Expression Profiles in Response to Fusarium Wilt Infection

Yan,

Su,

et al. 2024

Horticulturae

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Fusarium wilt in Cymbidium ensifolium, caused by Fusarium oxysporum, is highly contagious and poses a severe hazard. It significantly reduces the ornamental value of C. ensifolium and causes substantial economic losses in agricultural production. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are key regulatory factors in plant disease resistance responses, playing vital roles in defending against pathogen invasions. In our study, we conducted a comprehensive analysis of the NBS-LRR gene family in the genome of Cymbidium ensifolium. Phylogenetic analysis identified a total of 31 NBS-LRR genes encoding NB-ARC proteins, which were categorized into five classes (CNL, CN, NL, N, RNL) based on their protein structural domains. These genes were found to be unevenly distributed across eight chromosomes. Physicochemical analysis revealed significant variances in molecular weight and sequence length among the family members. Subcellular localization results indicated that most genes primarily reside in the cytoplasm and cell membrane, suggesting that the primary sites of disease resistance responses may be the cell membrane and cyto-plasm. Furthermore, noticeable disparities were observed in gene structures and conserved motifs among different categories of family genes. Promoter analysis indicated that cis-regulatory elements are mainly associated with plant stress, jasmonic acid, gibberellin, and other development-related factors, suggesting that CeNBS-LRR genes mainly resist external stress through hormones such as abscisic acid and jasmonic acid. We characterized twenty-seven CeNBS-LRR gene expression patterns of healthy C. ensifolium at different periods after Fusarium wilt infection, and found that those genes exhibit a temporospatial expression pattern, and that their expression is also responsive to Fusarium wilt infection. By analyzing the expression pattern via transcriptome and qRT-PCR, we speculated that JL006442 and JL014305 may play key roles in resisting Fusarium wilt. This study lays the groundwork and holds considerable significance as a reference for identifying disease-resistant genes and facilitating genetic breeding in C. ensifolium.

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Genome-Wide Analysis of the TIFY Gene Family in Three Cymbidium Species and Its Response to Heat Stress in Cymbidium goeringii

Zhang,

He,

Huang

et al. 2024

Horticulturae

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The TIFY family is a plant-specific gene family that is involved in regulating a variety of plant processes, including developmental and defense responses. The Cymbidium species have certain ornamental and ecological value. However, the characteristics and functions of TIFY genes in Cymbidium remain poorly understood. This study conducted a genome analysis of the TIFY gene family in Cymbidium goeringii, C. ensifolium, and C. sinense and investigated their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns under heat stress in C. goeringii. C. goeringii (26), C. ensifolium (19), and C. sinense (21). A total of 66 TIFY genes were identified, and they were classified into four subfamilies (JAZ, ZML, PPD, and TIFY) based on their systematic evolutionary relationships. Sequence analysis showed that TIFYs contained a conserved TIFY domain and that genes within the same subfamily had structural similarity. Analysis of cis-regulatory elements revealed that these genes contain numerous light-responsive elements and stress-responsive elements. We subjected C. goeringii (16 h light/8 h dark) to 24 h of 38 °C high-temperature stress in a climate chamber. Additionally, results from RT-qPCR experiments showed that under heat stress, the expression levels of eight genes in C. goeringii show significant differences. Among them, the JAZ subfamily exhibited the strongest response to heat stress, initially showing upregulation followed by a downregulation trend. In conclusion, this study investigated the role of TIFY genes in three Cymbidium species, providing insights into C. goeringii under heat stress.

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Transcriptome analysis reveals the key pathways and candidate genes involved in salt stress responses in Cymbidium ensifolium leaves

Cited by 3 publications

References 106 publications

General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature

General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature

Genome-Wide Identification of Nucleotide-Binding Site–Leucine-Rich Repeat Gene Family in Cymbidium ensifolium and Expression Profiles in Response to Fusarium Wilt Infection

Genome-Wide Analysis of the TIFY Gene Family in Three Cymbidium Species and Its Response to Heat Stress in Cymbidium goeringii

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