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Shilpha J, Lee J, Kwon JS, Lee HA, Nam JY, Jang H, Kang WH. An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions. PLANT METHODS 2024; 20:99. [PMID: 38951818 PMCID: PMC11218159 DOI: 10.1186/s13007-024-01227-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Dual RNA sequencing is a powerful tool that enables a comprehensive understanding of the molecular dynamics underlying plant-microbe interactions. RNA sequencing (RNA-seq) poses technical hurdles in the transcriptional analysis of plant-bacterial interactions, especially in bacterial transcriptomics, owing to the presence of abundant ribosomal RNA (rRNA), which potentially limits the coverage of essential transcripts. Therefore, to achieve cost-effective and comprehensive sequencing of the bacterial transcriptome, it is imperative to devise efficient methods for eliminating rRNA and enhancing the proportion of bacterial mRNA. In this study, we modified a strand-specific dual RNA-seq method with the goal of enriching the proportion of bacterial mRNA in the bacteria-infected plant samples. The enriched method involved the sequential separation of plant mRNA by poly A selection and rRNA removal for bacterial mRNA enrichment followed by strand specific RNA-seq library preparation steps. We assessed the efficiency of the enriched method in comparison to the conventional method by employing various plant-bacterial interactions, including both host and non-host resistance interactions with pathogenic bacteria, as well as an interaction with a beneficial rhizosphere associated bacteria using pepper and tomato plants respectively. RESULTS In all cases of plant-bacterial interactions examined, an increase in mapping efficiency was observed with the enriched method although it produced a lower read count. Especially in the compatible interaction with Xanthmonas campestris pv. Vesicatoria race 3 (Xcv3), the enriched method enhanced the mapping ratio of Xcv3-infected pepper samples to its own genome (15.09%; 1.45-fold increase) and the CDS (8.92%; 1.49-fold increase). The enriched method consistently displayed a greater number of differentially expressed genes (DEGs) than the conventional RNA-seq method at all fold change threshold levels investigated, notably during the early stages of Xcv3 infection in peppers. The Gene Ontology (GO) enrichment analysis revealed that the DEGs were predominantly enriched in proteolysis, kinase, serine type endopeptidase and heme binding activities. CONCLUSION The enriched method demonstrated in this study will serve as a suitable alternative to the existing RNA-seq method to enrich bacterial mRNA and provide novel insights into the intricate transcriptomic alterations within the plant-bacterial interplay.
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Affiliation(s)
- Jayabalan Shilpha
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Ji-Su Kwon
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hyun-Ah Lee
- Division of Smart Horticulture, Yonam College, Cheonan, 31005, Republic of Korea
| | - Jae-Young Nam
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hakgi Jang
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Won-Hee Kang
- Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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Kim N, Lee J, Yeom SI, Kang NJ, Kang WH. The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper. Sci Data 2024; 11:381. [PMID: 38615136 PMCID: PMC11016105 DOI: 10.1038/s41597-024-03239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/05/2024] [Indexed: 04/15/2024] Open
Abstract
Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.
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Affiliation(s)
- Nayoung Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Junesung Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea
| | - Nam-Jun Kang
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea
| | - Won-Hee Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea.
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea.
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Lee J, Yeom SI. Global co-expression network for key factor selection on environmental stress RNA-seq dataset in Capsicum annuum. Sci Data 2023; 10:692. [PMID: 37828130 PMCID: PMC10570317 DOI: 10.1038/s41597-023-02592-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Environmental stresses significantly affect plant growth, development, and productivity. Therefore, a deeper understanding of the underlying stress responses at the molecular level is needed. In this study, to identify critical genetic factors associated with environmental stress responses, the entire 737.3 Gb clean RNA-seq dataset across abiotic, biotic stress, and phytohormone conditions in Capsicum annuum was used to perform individual differentially expressed gene analysis and to construct gene co-expression networks for each stress condition. Subsequently, gene networks were reconstructed around transcription factors to identify critical factors involved in the stress responses, including the NLR gene family, previously implicated in resistance. The abiotic and biotic stress networks comprise 233 and 597 hubs respectively, with 10 and 89 NLRs. Each gene within the NLR groups in the network exhibited substantial expression to particular stresses. The integrated analysis strategy of the transcriptome network revealed potential key genes for complex environmental conditions. Together, this could provide important clues to uncover novel key factors using high-throughput transcriptome data in other species as well as plants.
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Affiliation(s)
- Junesung Lee
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea.
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de Aguiar ÉS, Dias AN, Sousa RM, Germano TA, de Sousa RO, Miranda RDS, Costa JH, dos Santos CP. Genome and Transcriptome Analyses of Genes Involved in Ascorbate Biosynthesis in Pepper Indicate Key Genes Related to Fruit Development, Stresses, and Phytohormone Exposures. PLANTS (BASEL, SWITZERLAND) 2023; 12:3367. [PMID: 37836106 PMCID: PMC10574469 DOI: 10.3390/plants12193367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/10/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Pepper (Capsicum annuum L.) is a vegetable consumed worldwide, primarily used for vitamin C uptake and condiment purposes. Ascorbate (Asc) is a multifunctional metabolite, acting as an antioxidant and enzymatic cofactor involved in multiple cellular processes. Nevertheless, there is no evidence about the contribution of biosynthesis pathways and regulatory mechanisms responsible for Asc reserves in pepper plants. Here, we present a genome- and transcriptome-wide investigation of genes responsible for Asc biosynthesis in pepper during fruit development, stresses, and phytohormone exposures. A total of 21 genes, scattered in ten of twelve pepper chromosomes were annotated. Gene expression analyses of nine transcriptomic experiments supported the primary role of the L-galactose pathway in the Asc-biosynthesizing process, given its constitutive, ubiquitous, and high expression profile observed in all studied conditions. However, genes from alternative pathways generally exhibited low expression or were unexpressed and appeared to play some secondary role under specific stress conditions and phytohormone treatments. Taken together, our findings provide a deeper spatio-temporal understanding of expression levels of genes involved in Asc biosynthesis, and they highlight GGP2, GME1 and 2, and GalLDH members from L-galactose pathway as promising candidates for future wet experimentation, addressing the attainment of increase in ascorbate content of peppers and other crops.
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Affiliation(s)
- Évelyn Silva de Aguiar
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
| | - Abigailde Nascimento Dias
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Raquel Mendes Sousa
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
| | - Thais Andrade Germano
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Renato Oliveira de Sousa
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
| | - Rafael de Souza Miranda
- Postgraduate Program in Agricultural Sciences, Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, Piauí, Brazil; (R.O.d.S.); (R.d.S.M.)
- Plant Science Department, Federal University of Piauí, Teresina 64049-550, Piauí, Brazil
| | - José Hélio Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Ceará, Brazil; (T.A.G.); (J.H.C.)
| | - Clesivan Pereira dos Santos
- Postgraduate Program in Environmental Sciences, Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil;
- Center of Sciences of Chapadinha, Federal University of Maranhão, Boa Vista, Chapadinha 65500-000, Maranhão, Brazil; (A.N.D.); (R.M.S.)
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Hao Y, Dong Z, Zhao Y, Tang W, Wang X, Li J, Wang L, Hu Y, Fang L, Guan X, Gu F, Liu Z, Zhang Z. Phylogenomic analysis of cytochrome P450 multigene family and its differential expression analysis in pepper ( Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1078377. [PMID: 36561456 PMCID: PMC9763298 DOI: 10.3389/fpls.2022.1078377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Plant cytochrome P450 is a multifamily enzyme widely involved in biochemical reactions for the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds. Pepper (Capsicum annuum L.) is an economically important plant. A comprehensive identification and characterization of P450 genes would provide valuable information on the evolutionary relationships of genes and their functional characteristics. In this study, we identified P450 genes in pepper with the aid of bioinformatics methods to investigate the phylogenetic relation, gene structure, chromosomal localization, duplicated events, and collinearity among Solanaceae species. We identified and classified 478 genes of P450 from the pepper genome into two major clades and nine subfamilies through phylogenetic analysis. Massive duplication events were found in the P450 gene family, which may explain the expansion of the P450 gene family. In addition, we also found that these duplication genes may have undergone strict purification selection during evolution. Gene expression analysis showed that some P450 genes that belong to clan 71 in pepper may play an important role in placenta and pericarp development. Through quantitative real-time polymerase chain reaction and transcriptome analysis, we also found that many P450 genes were related to defensive and phytohormone response in pepper. These findings provide insight for further studies to identify the biological functions of the P450 genes in pepper.
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Affiliation(s)
- Yupeng Hao
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeyu Dong
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yongyan Zhao
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenchen Tang
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Jun Li
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Luyao Wang
- Hainan Institute, Zhejiang University, Sanya, China
| | - Yan Hu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Fang
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Guan
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fenglin Gu
- Spice and Beverage Research Institute, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Haikou, China
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Kang WH, Lee J, Koo N, Kwon JS, Park B, Kim YM, Yeom SI. Universal gene co-expression network reveals receptor-like protein genes involved in broad-spectrum resistance in pepper (Capsicum annuum L.). HORTICULTURE RESEARCH 2022; 9:uhab003. [PMID: 35043174 PMCID: PMC8968494 DOI: 10.1093/hr/uhab003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 09/08/2021] [Indexed: 05/21/2023]
Abstract
Receptor-like proteins (RLPs) on plant cells have been implicated in immune responses and developmental processes. Although hundreds of RLP genes have been identified in plants, only a few RLPs have been functionally characterized in a limited number of plant species. Here, we identified RLPs in the pepper (Capsicum annuum) genome and performed comparative transcriptomics coupled with the analysis of conserved gene co-expression networks (GCNs) to reveal the role of core RLP regulators in pepper-pathogen interactions. A total of 102 RNA-seq datasets of pepper plants infected with four pathogens were used to construct CaRLP-targeted GCNs (CaRLP-GCNs). Resistance-responsive CaRLP-GCNs were merged to construct a universal GCN. Fourteen hub CaRLPs, tightly connected with defense-related gene clusters, were identified in eight modules. Based on the CaRLP-GCNs, we evaluated whether hub CaRLPs in the universal GCN are involved in the biotic stress response. Of the nine hub CaRLPs tested by virus-induced gene silencing, three genes (CaRLP264, CaRLP277, and CaRLP351) showed defense suppression with less hypersensitive response-like cell death in race-specific and non-host resistance response to viruses and bacteria, respectively, and consistently enhanced susceptibility to Ralstonia solanacearum and/or Phytophthora capsici. These data suggest that key CaRLPs are involved in the defense response to multiple biotic stresses and can be used to engineer a plant with broad-spectrum resistance. Together, our data show that generating a universal GCN using comprehensive transcriptome datasets can provide important clues to uncover genes involved in various biological processes.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828,
Republic of Korea
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ji-Su Kwon
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Boseul Park
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Genome Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828,
Republic of Korea
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
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Kalapos B, Juhász C, Balogh E, Kocsy G, Tóbiás I, Gullner G. Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction. Sci Rep 2021; 11:20680. [PMID: 34667194 PMCID: PMC8526828 DOI: 10.1038/s41598-021-00002-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Upon virus infections, the rapid and comprehensive transcriptional reprogramming in host plant cells is critical to ward off virus attack. To uncover genes and defense pathways that are associated with virus resistance, we carried out the transcriptome-wide Illumina RNA-Seq analysis of pepper leaves harboring the L3 resistance gene at 4, 8, 24 and 48 h post-inoculation (hpi) with two tobamoviruses. Obuda pepper virus (ObPV) inoculation led to hypersensitive reaction (incompatible interaction), while Pepper mild mottle virus (PMMoV) inoculation resulted in a systemic infection without visible symptoms (compatible interaction). ObPV induced robust changes in the pepper transcriptome, whereas PMMoV showed much weaker effects. ObPV markedly suppressed genes related to photosynthesis, carbon fixation and photorespiration. On the other hand, genes associated with energy producing pathways, immune receptors, signaling cascades, transcription factors, pathogenesis-related proteins, enzymes of terpenoid biosynthesis and ethylene metabolism as well as glutathione S-transferases were markedly activated by ObPV. Genes related to photosynthesis and carbon fixation were slightly suppressed also by PMMoV. However, PMMoV did not influence significantly the disease signaling and defense pathways. RNA-Seq results were validated by real-time qPCR for ten pepper genes. Our findings provide a deeper insight into defense mechanisms underlying tobamovirus resistance in pepper.
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Affiliation(s)
- Balázs Kalapos
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Brunszvik utca 2, Martonvásár, 2462, Hungary
| | - Csilla Juhász
- Plant Protection Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Herman Ottó út 15, Budapest, 1022, Hungary
| | - Eszter Balogh
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Brunszvik utca 2, Martonvásár, 2462, Hungary
| | - Gábor Kocsy
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Brunszvik utca 2, Martonvásár, 2462, Hungary
| | - István Tóbiás
- Plant Protection Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Herman Ottó út 15, Budapest, 1022, Hungary
| | - Gábor Gullner
- Plant Protection Institute, Centre for Agricultural Research, Eötvös Lóránt Research Network (ELKH), Herman Ottó út 15, Budapest, 1022, Hungary.
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Kang WH, Park B, Lee J, Yeom SI. Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum. PLANTS (BASEL, SWITZERLAND) 2021; 10:972. [PMID: 34068172 PMCID: PMC8152994 DOI: 10.3390/plants10050972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in response to multiple biotic stresses. To further understand the role of CaRLPs in plant growth and development, we analyzed expression patterns of all CaRLPs from various pepper tissues and developmental stages using RNA-seq. Ten CaRLP genes were selected for further analysis according to transcript levels with hierarchical clustering. The selected CaRLP genes displayed similarity of motifs within the same groups and structures typical of RLPs. To examine RLP function in growth and development, we performed loss-of-function analysis using a virus-induced gene silencing system. Three of the ten tested CaRLPs (CaRLP238, 253, and 360) in silenced plants exhibited phenotypic alteration with growth retardation compared to controls. All three gene-silenced peppers showed significant differences in root dry weight. Only CaRLP238 had significant differences in both root and shoot dry weight. Our results suggest that CaRLPs may play important roles in regulation of plant growth and development as well as function in defense responses to biotic stresses in the RLP gene family.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Boseul Park
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea;
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
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Lee J, Nam JY, Jang H, Kim N, Kim YM, Kang WH, Yeom SI. Comprehensive transcriptome resource for response to phytohormone-induced signaling in Capsicum annuum L. BMC Res Notes 2020; 13:440. [PMID: 32943083 PMCID: PMC7499990 DOI: 10.1186/s13104-020-05281-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in major crops. Here, we aimed to provide transcriptome dataset using RNA sequencing for phytohormone-induced signaling in plant. DATA DESCRIPTION We used high-throughput RNA sequencing profiling to investigate the pepper plant response to treatment with four major phytohormones (salicylic acid, jasmonic acid, ethylene, and abscisic acid). This dataset yielded 78 samples containing three biological replicates per six different time points for each treatment and the control, constituting 187.8 Gb of transcriptome data (2.4 Gb of each sample). This comprehensive parallel transcriptome data provides valuable information for understanding the relationships and molecular networks that regulate the expression of phytohormone-related genes involved in plant developments and environmental stress adaptation.
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Affiliation(s)
- Junesung Lee
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Jae-Young Nam
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Hakgi Jang
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Nayoung Kim
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Yong-Min Kim
- Genome Engineering Research Center, Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141 Republic of Korea
| | - Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
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