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Marques I, Fernandes I, Paulo OS, Batista D, Lidon FC, Rodrigues AP, Partelli FL, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Transcriptomic Analyses Reveal That Coffea arabica and Coffea canephora Have More Complex Responses under Combined Heat and Drought than under Individual Stressors. Int J Mol Sci 2024; 25:7995. [PMID: 39063237 PMCID: PMC11277005 DOI: 10.3390/ijms25147995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/14/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Increasing exposure to unfavorable temperatures and water deficit imposes major constraints on most crops worldwide. Despite several studies regarding coffee responses to abiotic stresses, transcriptome modulation due to simultaneous stresses remains poorly understood. This study unravels transcriptomic responses under the combined action of drought and temperature in leaves from the two most traded species: Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu. Substantial transcriptomic changes were found, especially in response to the combination of stresses that cannot be explained by an additive effect. A large number of genes were involved in stress responses, with photosynthesis and other physiologically related genes usually being negatively affected. In both genotypes, genes encoding for protective proteins, such as dehydrins and heat shock proteins, were positively regulated. Transcription factors (TFs), including MADS-box genes, were down-regulated, although responses were genotype-dependent. In contrast to Icatu, only a few drought- and heat-responsive DEGs were recorded in CL153, which also reacted more significantly in terms of the number of DEGs and enriched GO terms, suggesting a high ability to cope with stresses. This research provides novel insights into the molecular mechanisms underlying leaf Coffea responses to drought and heat, revealing their influence on gene expression.
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Affiliation(s)
- Isabel Marques
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre (CEF), Associate Laboratory TERRA, School of Agriculture (ISA), University of Lisbon, 1349-017 Lisboa, Portugal; (A.P.R.); (J.C.R.)
| | - Isabel Fernandes
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (O.S.P.); (D.B.)
| | - Octávio S. Paulo
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (O.S.P.); (D.B.)
| | - Dora Batista
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (O.S.P.); (D.B.)
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture (ISA), University of Lisbon, 1349-017 Lisboa, Portugal
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal;
| | - Ana P. Rodrigues
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre (CEF), Associate Laboratory TERRA, School of Agriculture (ISA), University of Lisbon, 1349-017 Lisboa, Portugal; (A.P.R.); (J.C.R.)
| | - Fábio L. Partelli
- Centro Universitário do Norte do Espírito Santo (CEUNES), Departmento Ciências Agrárias e Biológicas (DCAB), Universidade Federal Espírito Santo (UFES), São Mateus 29932-540, ES, Brazil;
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-900, MG, Brazil;
| | - Ana I. Ribeiro-Barros
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre (CEF), Associate Laboratory TERRA, School of Agriculture (ISA), University of Lisbon, 1349-017 Lisboa, Portugal; (A.P.R.); (J.C.R.)
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal;
| | - José C. Ramalho
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre (CEF), Associate Laboratory TERRA, School of Agriculture (ISA), University of Lisbon, 1349-017 Lisboa, Portugal; (A.P.R.); (J.C.R.)
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal;
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Yu H, Bi X, Li Z, Fu X, Li Y, Li Y, Yang Y, Liu D, Li G, Dong W, Hu F. Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L. Genes (Basel) 2024; 15:459. [PMID: 38674393 PMCID: PMC11050144 DOI: 10.3390/genes15040459] [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: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.
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Affiliation(s)
- Haohao Yu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xiaofei Bi
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Zhongxian Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yang Yang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Dexin Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Wenjiang Dong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
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Bi X, Yu H, Hu F, Fu X, Li Y, Li Y, Yang Y, Liu D, Li G, Shi R, Dong W. A Systematic Analysis of the Correlation between Flavor Active Differential Metabolites and Multiple Bean Ripening Stages of Coffea arabica L. Molecules 2023; 29:180. [PMID: 38202762 PMCID: PMC10779739 DOI: 10.3390/molecules29010180] [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: 10/24/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Coffee cherries contain a crucial flavor-precursor and chemical substances influencing roasted bean quality, yet limited knowledge exists on metabolite changes during cherry ripening. Our study identified 1078 metabolites, revealing 46 core differential metabolites using a KEGG pathway analysis. At the GF vs. ROF stage, amino acid synthesis dominated; ROF vs. BRF featured nucleotide catabolism; BRF vs. PRF exhibited glycoside and flavonoid synthesis; and PRF vs. PBF involved secondary metabolite synthesis and catabolism. The PRF stage emerged as the optimal cherry-harvesting period. A correlation analysis identified core differential metabolites strongly linked to taste indicators, suggesting their potential as taste markers. Notably, nucleotides and derivatives exhibited significant negative correlations with glycosides and flavonoids during ripening. This research systematically analyzed flavor and active substances in green coffee beans during cherry ripening, offering valuable insights into substance formation in Coffea arabica L.
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Affiliation(s)
- Xiaofei Bi
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Haohao Yu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Yang Yang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Dexin Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (X.B.); (H.Y.); (F.H.); (X.F.); (Y.L.); (Y.L.); (Y.Y.); (D.L.); (G.L.)
| | - Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Wenjiang Dong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
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Wei F, Wan R, Shi Z, Ma W, Wang H, Chen Y, Bo J, Li Y, An W, Qin K, Cao Y. Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji ( Lycium barbarum L.) Fruit Ripening. PLANTS (BASEL, SWITZERLAND) 2023; 12:2791. [PMID: 37570945 PMCID: PMC10421014 DOI: 10.3390/plants12152791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Carotenoids in goji (Lycium barbarum L.) have excellent health benefits, but the underlying mechanism of carotenoid synthesis and color formation in goji fruit ripening is still unclear. The present study uses transcriptomics and metabolomics to investigate carotenoid biosynthesis and color formation differences in N1 (red fruit) and N1Y (yellow fruit) at three stages of ripening. Twenty-seven carotenoids were identified in N1 and N1Y fruits during the M1, M2, and M3 periods, with the M2 and M3 periods being critical for the difference in carotenoid and color between N1 and N1Y fruit. Weighted gene co-expression network analysis (WGCNA), gene trend analysis, and correlation analysis suggest that PSY1 and ZDS16 may be important players in the synthesis of carotenoids during goji fruit ripening. Meanwhile, 63 transcription factors (TFs) were identified related to goji fruit carotenoid biosynthesis. Among them, four TFs (CMB1-1, WRKY22-1, WRKY22-3, and RAP2-13-like) may have potential regulatory relationships with PSY1 and ZDS16. This work sheds light on the molecular network of carotenoid synthesis and explains the differences in carotenoid accumulation in different colored goji fruits.
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Affiliation(s)
- Feng Wei
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
- Ningxia State Farm A&F Technology Central, Yinchuan 750002, China; (W.M.); (H.W.); (Y.C.); (J.B.)
| | - Ru Wan
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
| | - Zhigang Shi
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
| | - Wenli Ma
- Ningxia State Farm A&F Technology Central, Yinchuan 750002, China; (W.M.); (H.W.); (Y.C.); (J.B.)
| | - Hao Wang
- Ningxia State Farm A&F Technology Central, Yinchuan 750002, China; (W.M.); (H.W.); (Y.C.); (J.B.)
| | - Yongwei Chen
- Ningxia State Farm A&F Technology Central, Yinchuan 750002, China; (W.M.); (H.W.); (Y.C.); (J.B.)
| | - Jianhua Bo
- Ningxia State Farm A&F Technology Central, Yinchuan 750002, China; (W.M.); (H.W.); (Y.C.); (J.B.)
| | - Yunxiang Li
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
| | - Wei An
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
| | - Ken Qin
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
| | - Youlong Cao
- Wolfberry Engineering Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (R.W.); (Y.L.); (W.A.); (K.Q.); (Y.C.)
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