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Shi M, Savoi S, Sarah G, Soriano A, Weber A, Torregrosa L, Romieu C. Vitis rotundifolia Genes Introgressed with RUN1 and RPV1: Poor Recombination and Impact on V. vinifera Berry Transcriptome. PLANTS (BASEL, SWITZERLAND) 2024; 13:2095. [PMID: 39124212 PMCID: PMC11314213 DOI: 10.3390/plants13152095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Thanks to several Vitis vinifera backcrosses with an initial V. vinifera L. × V. rotundifolia (previously Muscadinia rotundifolia) interspecific cross, the MrRUN1/MrRPV1 locus (resistance to downy and powdery mildews) was introgressed in genotypes phenotypically close to V. vinifera varieties. To check the consequences of introgressing parts of the V. rotundifolia genome on gene expression during fruit development, we conducted a comparative RNA-seq study on single berries from different V. vinifera cultivars and V. vinifera × V. rotundifolia hybrids, including 'G5' and two derivative microvine lines, 'MV102' (resistant) and 'MV32' (susceptible) segregating for the MrRUN1/RPV1 locus. RNA-Seq profiles were analyzed on a comprehensive set of single berries from the end of the herbaceous plateau to the ripe stage. Pair-end reads were aligned both on V. vinifera PN40024.V4 reference genome, V. rotundifolia cv 'Trayshed' and cv 'Carlos', and to the few resistance genes from the original V. rotundifolia cv '52' parent available at NCBI. Weighted Gene Co-expression Network Analysis (WGCNA) led to classifying the differentially expressed genes into 15 modules either preferentially correlated with resistance or berry phenology and composition. Resistance positively correlated transcripts predominantly mapped on the 4-5 Mb distal region of V. rotundifolia chromosome 12 beginning with the MrRUN1/MrRPV1 locus, while the negatively correlated ones mapped on the orthologous V. vinifera region, showing this large extremity of LG12 remained recalcitrant to internal recombination during the successive backcrosses. Some constitutively expressed V. rotundifolia genes were also observed at lower densities outside this region. Genes overexpressed in developing berries from resistant accessions, either introgressed from V. rotundifolia or triggered by these in the vinifera genome, spanned various functional groups, encompassing calcium signal transduction, hormone signaling, transcription factors, plant-pathogen-associated interactions, disease resistance proteins, ROS and phenylpropanoid biosynthesis. This transcriptomic insight provides a foundation for understanding the disease resistance inherent in these hybrid cultivars and suggests a constitutive expression of NIR NBS LRR triggering calcium signaling. Moreover, these results illustrate the magnitude of transcriptomic changes caused by the introgressed V. rotundifolia background in backcrossed hybrids, on a large number of functions largely exceeding the ones constitutively expressed in single resistant gene transformants.
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Affiliation(s)
- Mengyao Shi
- UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34090 Montpellier, France; (M.S.); (G.S.); (A.S.); (A.W.)
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy;
| | - Gautier Sarah
- UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34090 Montpellier, France; (M.S.); (G.S.); (A.S.); (A.W.)
- UMT Geno-Vigne, IFV-INRAE-Institute Agro, 34060 Montpellier, France;
| | - Alexandre Soriano
- UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34090 Montpellier, France; (M.S.); (G.S.); (A.S.); (A.W.)
| | - Audrey Weber
- UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34090 Montpellier, France; (M.S.); (G.S.); (A.S.); (A.W.)
| | - Laurent Torregrosa
- UMT Geno-Vigne, IFV-INRAE-Institute Agro, 34060 Montpellier, France;
- LEPSE, University Montpellier, CIRAD, INRAE, Institute Agro, 34060 Montpellier, France
| | - Charles Romieu
- UMR AGAP Institute, University Montpellier, CIRAD, INRAE, Institute Agro, 34090 Montpellier, France; (M.S.); (G.S.); (A.S.); (A.W.)
- UMT Geno-Vigne, IFV-INRAE-Institute Agro, 34060 Montpellier, France;
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Gao H, Xue J, Yuan L, Sun Y, Song Y, Zhang C, Li R, Jia X. Systematic characterization of CsbZIP transcription factors in Camelina sativa and functional analysis of CsbZIP-A12 mediating regulation of unsaturated fatty acid-enriched oil biosynthesis. Int J Biol Macromol 2024; 270:132273. [PMID: 38734348 DOI: 10.1016/j.ijbiomac.2024.132273] [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: 12/28/2023] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The basic leucine zipper (bZIP) transcription factors (TFs) function importantly in numerous life processes in plants. However, bZIP members and their biological roles remain unknown in Camelina sativa, a worldwide promising oil crop. Here, 220 CsbZIP proteins were identified in camelina and classified into thirteen groups. Two and 347 pairs of tandem and segmental duplication genes were detected to be underwent purification selection, with segmental duplication as the main driven-force of CsbZIP gene family expansion. Most CsbZIP genes displayed a tissue-specific expression pattern. Particularly, CsbZIP-A12 significantly positively correlated with many FA/oil biosynthesis-related genes, indicating CsbZIP-A12 may regulate lipid biosynthesis. Notably, yeast one-hybrid (Y1H), β-Glucuronidase (GUS), dual-luciferase (LUC) and EMSA assays evidenced that CsbZIP-A12 located in nucleus interacted with the promoters of CsSAD2-3 and CsFAD3-3 genes responsible for unsaturated fatty acid (UFA) synthesis, thus activating their transcriptions. Overexpression of CsbZIP-A12 led to an increase of total lipid by 3.275 % compared to the control, followed with oleic and α-linolenic acid levels enhanced by 3.4 % and 5.195 %, and up-regulated the expressions of CsSAD2-3, CsFAD3-3 and CsPDAT2-3 in camelina seeds. Furthermore, heterogeneous expression of CsbZIP-A12 significantly up-regulated the expressions of NtSAD2, NtFAD3 and NtPDAT genes in tobacco plants, thereby improving the levels of total lipids and UFAs in both leaves and seeds without negative effects on other agronomic traits. Together, our findings suggest that CsbZIP-A12 upregulates FA/oil biosynthesis by activating CsSAD2-3 and CsFAD3-3 as well as possible other related genes. These data lay a foundation for further functional analyses of CsbZIPs, providing new insights into the TF-based lipid metabolic engineering to increase vegetable oil yield and health-beneficial quality in oilseeds.
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Affiliation(s)
- Huiling Gao
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China
| | - Jinai Xue
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China
| | - Lixia Yuan
- College of Biological Science and Technology, Jinzhong University, Jinzhong, Shanxi, China
| | - Yan Sun
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China
| | - Yanan Song
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China
| | - Chunhui Zhang
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China
| | - Runzhi Li
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China.
| | - Xiaoyun Jia
- College of Agronomy/Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Special Crops, Taigu, Shanxi, China.
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Ren Y, Sadeghnezhad E, Leng X, Pei D, Dong T, Zhang P, Gong P, Jia H, Fang J. Assessment of 'Cabernet Sauvignon' Grape Quality Half-Véraison to Maturity for Grapevines Grown in Different Regions. Int J Mol Sci 2023; 24:ijms24054670. [PMID: 36902101 PMCID: PMC10002954 DOI: 10.3390/ijms24054670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Grapes are widely cultivated around the world and their quality has distinct regional characteristics. In this study, the qualitative characteristics of the 'Cabernet Sauvignon' grape variety in seven regions, from half-véraison to maturity, were analyzed comprehensively at physiological and transcriptional levels. The results indicated that the quality traits of 'Cabernet Sauvignon' grapes in different regions were significantly different with obvious regionality. Total phenols, anthocyanins, and titratable acids were the main factors of the regionality of berry quality, which were very sensitive to changes in the environment. It should be noted that the changes in titrating acids and total anthocyanin of berries vary greatly from half-véraison to maturity between regions. Moreover, the transcriptional analysis showed that the co-expressed genes between regions characterized the core transcriptome of berry development, while the unique genes of each region reflected the regionality of berries. The differentially expressed genes (DEGs) between half-véraison and maturity can be used to demonstrate that the environment of the regions could promote or inhibit gene expression. The functional enrichment suggested that these DEGs help to understand the interpretation of the plasticity of the quality composition of grapes according to the environment. Taken together, the information generated by this study could contribute to the development of viticultural practices aimed at making better use of native varieties for the development of wines with regional characteristics.
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Affiliation(s)
- Yanhua Ren
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangpeng Leng
- Horticultural College, Qingdao Agricultural University, Qingdao 266109, China
| | - Dan Pei
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Peian Zhang
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Peijie Gong
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, Horticultural College, Nanjing Agricultural University, Nanjing 210095, China
- Horticultural College, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence:
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Differentially expression analyses in fruit of cultivated and wild species of grape and peach. Sci Rep 2023; 13:1997. [PMID: 36737657 PMCID: PMC9898514 DOI: 10.1038/s41598-023-29025-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Through agronomic traits and sequencing data, the cultivated and wild varieties of grapes and peaches were analyzed and compared in terms of fruit size, fruit flavor, fruit resistance, and fruit color. Cultivated grapes and peaches have advantages in fruit size, soluble sugar content, sugar and acid ratio, etc. Wild grapes and peaches have utility value in resistance. The results showed that there were 878 and 301 differentially expressed genes in cultivated and wild grapes and peaches in the three growth stages, respectively based on the next-generation sequencing study. Ten and twelve genes related to the differences between cultivated and wild grapes and peaches were found respectively. Among them, three genes, namely chalcone synthase (CHS), glutathione S-transferase (GST) and malate dehydrogenase (MDH1) were present in both cultivated and wild grapes and peaches.
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D'Incà E, Foresti C, Orduña L, Amato A, Vandelle E, Santiago A, Botton A, Cazzaniga S, Bertini E, Pezzotti M, Giovannoni J, Vrebalov J, Matus JT, Tornielli GB, Zenoni S. The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine. PLANT PHYSIOLOGY 2023:kiad050. [PMID: 36718552 DOI: 10.1093/plphys/kiad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/03/2022] [Accepted: 12/11/2022] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being up-regulated through a VviNAC60-VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologues to the NAC transcription factor AtNAP, VviNAC60 complemented the non-ripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase.
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Affiliation(s)
- Erica D'Incà
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Chiara Foresti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Alessandro Botton
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Italy
| | - Stefano Cazzaniga
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Edoardo Bertini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - James Giovannoni
- USDA-ARS Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Tower Road, Cornell Campus, Ithaca, NY 14853, USA
| | - Julia Vrebalov
- USDA-ARS Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Tower Road, Cornell Campus, Ithaca, NY 14853, USA
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | | | - Sara Zenoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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Identification of Key Genes Induced by Different Potassium Levels Provides Insight into the Formation of Fruit Quality in Grapes. Int J Mol Sci 2023; 24:ijms24021218. [PMID: 36674735 PMCID: PMC9866991 DOI: 10.3390/ijms24021218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Inadequate potassium (K) availability is a common abiotic stress that limits the growth and quality of fruit trees. Few studies have investigated the physiological and molecular responses of grapes at different potassium levels. In this study, an integrated approach was developed for grapevines grown at four different potassium fertilization levels [0 (K0-CK), 150 (K150), 300 (K300), and 450 (K450) g/plant] in combination with metabolite measurements and transcript analysis. The results showed that different K levels affected the accumulation of sugars and anthocyanins in the fruit. At 78 days after bloom (DAB), the K150, K300, and K450 treatments increased soluble sugar content by 37.39%, 31.10% and 32.59%, respectively, and anthocyanin content by 49.78%, 24.10%, and 13.06%, respectively, compared to K0. Weighted gene co-expression network analysis (WGCNA) of DEGs identified a network of 11 grapevines involved. During fruit development, potassium application promoted the accumulation of anthocyanins and sugars in fruit by regulating the up-regulation of GST, AT, UFGT and SPS, HT, PK gene expressions. These results suggest that potassium deficiency inhibits anthocyanin and sugar metabolism. In addition, it promotes the up-regulation of KUP expression, which is the main cause of K accumulation in fruits. Together, our data revealed the molecular mechanism in response to different K levels during fruit quality formation and provides the scientific foundation for the improvement of fruit quality by adding K fertilizer.
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Savoi S, Santiago A, Orduña L, Matus JT. Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. FRONTIERS IN PLANT SCIENCE 2022; 13:937927. [PMID: 36340350 PMCID: PMC9630917 DOI: 10.3389/fpls.2022.937927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
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Varanasi A, Worthington M, Nelson L, Brown A, Chizk TM, Threlfall R, Howard L, Conner P, Figueroa-Balderas R, Massonnet M, Cantu D, Clark JR. Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia). G3 (BETHESDA, MD.) 2022; 12:6550507. [PMID: 35302606 PMCID: PMC9073687 DOI: 10.1093/g3journal/jkac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/09/2022] [Indexed: 01/27/2023]
Abstract
Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine glutathione S-transferase4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 126 breeding selections, 76 cultivars, and 359 progeny from 3 mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action. VrGST4 was expressed in skins of both black and bronze muscadines at similar levels. While nonsynonymous polymorphisms between black and bronze muscadines were discovered in VrGSTF12, another Type I GST-coding gene in the muscadine color locus, this gene was ruled out as a possible candidate for berry color because RNA sequencing indicated it is not expressed in berry skins at véraison from black or bronze genotypes. These results suggest that the bronze phenotype in muscadines is regulated by a mechanism distinct from the MybA gene cluster responsible for berry color variation in Vitis vinifera.
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Affiliation(s)
- Aruna Varanasi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Lacy Nelson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Autumn Brown
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Thomas Mason Chizk
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Renee Threlfall
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Luke Howard
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Patrick Conner
- Department of Horticulture, University of Georgia, Tifton, GA 31793, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - John R Clark
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
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Maestri S, Gambino G, Lopatriello G, Minio A, Perrone I, Cosentino E, Giovannone B, Marcolungo L, Alfano M, Rombauts S, Cantu D, Rossato M, Delledonne M, Calderón L. 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). BMC Genomics 2022; 23:159. [PMID: 35209840 PMCID: PMC8867635 DOI: 10.1186/s12864-022-08389-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 12/18/2022] Open
Abstract
Background ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08389-9.
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Affiliation(s)
- Simone Maestri
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Giulia Lopatriello
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Andrea Minio
- Department of Viticulture & Enology, University of California Davis, 595 Hilgard Lane, Davis, CA, 95616, USA
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Emanuela Cosentino
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Barbara Giovannone
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Massimiliano Alfano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Stephane Rombauts
- Department of Bioinformatics and Systems Biology, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium
| | - Dario Cantu
- Department of Viticulture & Enology, University of California Davis, 595 Hilgard Lane, Davis, CA, 95616, USA
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Luciano Calderón
- Instituto de Biología Agrícola de Mendoza (IBAM, CONICET-UNCuyo), Almirante Brown 500, M5528AHB. Chacras de Coria, Mendoza, Argentina.
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10
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Vannozzi A, Palumbo F, Magon G, Lucchin M, Barcaccia G. The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases. HORTICULTURE RESEARCH 2021; 8:200. [PMID: 34465729 PMCID: PMC8408131 DOI: 10.1038/s41438-021-00635-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human's genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.
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Affiliation(s)
- Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy.
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11
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Vondras AM, Lerno L, Massonnet M, Minio A, Rowhani A, Liang D, Garcia J, Quiroz D, Figueroa‐Balderas R, Golino DA, Ebeler SE, Al Rwahnih M, Cantu D. Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling. MOLECULAR PLANT PATHOLOGY 2021; 22:984-1005. [PMID: 34075700 PMCID: PMC8295520 DOI: 10.1111/mpp.13077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 05/14/2023]
Abstract
Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms influenced by host genotype, rootstock, environment, and which individual or combination of GLRaVs is present. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet Franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet Franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study characterized conserved and condition-dependent responses to GLRaV infection(s). Common responses to GLRaVs were reproduced in two consecutive years and occurred in plants grafted to different rootstocks in more than one infection condition. Though different infections were inconsistently distinguishable from one another, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of genes related to pathogen detection, abscisic acid (ABA) signalling, phenylpropanoid biosynthesis, and cytoskeleton remodelling. ABA, ABA glucose ester, ABA and hormone signalling-related gene expression, and the expression of genes in several transcription factor families differentiated the effects of GLRaVs in berries from Cabernet Franc grapevines grafted to different rootstocks. These results support that ABA participates in the shared responses to GLRaV infection and differentiates the responses observed in grapevines grafted to different rootstocks.
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Affiliation(s)
- Amanda M. Vondras
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Larry Lerno
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Andrea Minio
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Adib Rowhani
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dingren Liang
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jadran Garcia
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Daniela Quiroz
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Deborah A. Golino
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Susan E. Ebeler
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Maher Al Rwahnih
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
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12
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Wang G, Li X, Ye N, Huang M, Feng L, Li H, Zhang J. OsTPP1 regulates seed germination through the crosstalk with abscisic acid in rice. THE NEW PHYTOLOGIST 2021; 230:1925-1939. [PMID: 33629374 DOI: 10.1111/nph.17300] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Seed germination is essential for direct seeding in rice. It has been demonstrated that trehalose-6-phosphate phosphatase 1 (OsTPP1) plays roles in improving yield and stress tolerance in rice. In this study, the roles of OsTPP1 on seed germination in rice were investigated. The tpp1 mutant germinated slower than the wild-type (WT), which can be restored by exogenous trehalose. tpp1 seeds showed higher ABA content compared with WT seeds. The tpp1 mutant was hypersensitive to ABA and ABA catabolism inhibitor (Dinicozanole). Furthermore, two ABA catabolism genes were downregulated in the tpp1 mutant which were responsible for increased ABA concentrations, and exogenous trehalose increased transcripts of ABA catabolism genes, suggesting that OsTPP1 and ABA catabolism genes acted in the same signaling pathway. Further analysis showed that a transcription factor of OsGAMYB was an activator of OsTPP1, and expression of OsGAMYB was decreased by both the exogenous and endogenous ABA, subsequently reducing the expression of OsTPP1, which suggested a new signaling pathway required for seed germination in rice. In addition, ABA-responsive genes, especially OsABI5, were invoved in OsTPP1-mediated seed germination. Overall, our study provided new pathways in seed germination that OsTPP1 controlled seed germination through crosstalk with the ABA catabolism pathway.
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Affiliation(s)
- Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Xiaozheng Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Mingkun Huang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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13
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Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.). Sci Rep 2021; 11:10721. [PMID: 34021210 PMCID: PMC8140124 DOI: 10.1038/s41598-021-90141-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/07/2021] [Indexed: 12/14/2022] Open
Abstract
Peanut is one of the important oil and economic crops, among which the variegated testa peanut is a unique member. The molecular mechanisms underlying the pigment synthesis in variegated testa are still unclear. Differentially expressed genes (DEGs) in the flavonoid metabolism pathway in pigmented areas indicated that there were 27 DEGs highly related to the synthesis of variegated testa color among 1,050 DEGs. Of these 27, 13 were up-regulated and 14 were down-regulated, including 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs, and 9 MYBs. GO (Gene Ontology) analysis indicated that DEGs were similarly enriched in three branches. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis suggested flavonoid biosynthesis is the most direct metabolic pathway for the synthesis of testa variegation. The liquid chromatography–tandem mass spectrometry (LC–MS/MS) results showed that cyanidin and delphinidin were the primary metabolites that caused the color differences between the pigmented and the non-pigmented areas. Through the verification of 20 DEGs via qPCR, the results were consistent with transcriptome sequencing in four comparison groups. The results in this study lay the foundation for revealing the molecular regulation mechanisms of flavonoid synthesis in variegated testa peanut.
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14
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Liu W, Tang R, Zhang Y, Liu X, Gao Y, Dai Z, Li S, Wu B, Wang L. Genome-wide identification of B-box proteins and VvBBX44 involved in light-induced anthocyanin biosynthesis in grape (Vitis vinifera L.). PLANTA 2021; 253:114. [PMID: 33934247 DOI: 10.1007/s00425-021-03618-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/26/2021] [Indexed: 05/27/2023]
Abstract
Genome-wide identification, analysis and functional characterization of an unreported VvBBX gene showed a response to light and positive correlation with anthocyanin content, but also inhibition of light-induced anthocyanin synthesis. B-box (BBX) proteins are a class of zinc (Zn) finger transcription factors or regulators characterized by the presence of one or two BBX domains and play important roles in plant growth and development. However, the BBX genes' potential functions are insufficiently characterized in grape, a globally popular berry with high economic value. Here, 25 BBX family genes including a novel member (assigned VvBBX44) were identified genome widely in grape. The expression level of these VvBBXs were analyzed in 'Cabernet Sauvignon' (V. vinifera) stem, flower, leaf, tendril, petiole, and developing berries. The expression of VvBBX44 increased in developing 'Cabernet Sauvignon' berries. Its expression was inhibited in 'Jingxiu' and 'Muscat Hamburg' berry skin without sunlight. Furthermore, overexpression of VvBBX44 decreased the expression of LONG HYPOCOTYL 5 (VvHY5) and UDP-glucose flavonoid 3-O-glucosyltransferase (VvUFGT), and reduced the anthocyanin content in grape calli. Our results suggest that VvBBX44 may play an important role in grape berry coloring by directly repressing VvHY5 expression. This study provides new insights into the potential role of VvBBXs in berry development and light response and contributes to the understanding on the regulation mechanism of VvBBX44 in anthocyanin biosynthesis.
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Affiliation(s)
- Wenwen Liu
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Renkun Tang
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Yuyu Zhang
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Yingying Gao
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China
| | - Benhong Wu
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China.
| | - Lijun Wang
- Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
- LIA INNOGRAPE International Associated Laboratory, Beijing, 100093, People's Republic of China.
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15
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Zombardo A, Crosatti C, Bagnaresi P, Bassolino L, Reshef N, Puccioni S, Faccioli P, Tafuri A, Delledonne M, Fait A, Storchi P, Cattivelli L, Mica E. Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality. BMC Genomics 2020; 21:468. [PMID: 32641089 PMCID: PMC7341580 DOI: 10.1186/s12864-020-06795-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/25/2020] [Indexed: 12/19/2022] Open
Abstract
Background In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigating the effect of two different rootstocks (1103 Paulsen - P - and Mgt 101–14 - M) in comparison with not grafted plants - NGC - on transcriptome (RNA-seq and small RNA-seq) and chemical composition of berry skin in Pinot noir, and exploring the influence of rootstock-scion interaction on grape quality. Berry samples, collected at veraison and maturity, were investigated at transcriptional and biochemical levels to depict the impact of rootstock on berry maturation. Results RNA- and miRNA-seq analyses highlighted that, at veraison, the transcriptomes of the berry skin are extremely similar, while variations associated with the different rootstocks become evident at maturity, suggesting a greater diversification at transcriptional level towards the end of the ripening process. In the experimental design, resembling standard agronomic growth conditions, the vines grafted on the two different rootstocks do not show a high degree of diversity. In general, the few genes differentially expressed at veraison were linked to photosynthesis, putatively because of a ripening delay in not grafted vines, while at maturity the differentially expressed genes were mainly involved in the synthesis and transport of phenylpropanoids (e.g. flavonoids), cell wall loosening, and stress response. These results were supported by some differences in berry phenolic composition detected between grafted and not grafted plants, in particular in resveratrol derivatives accumulation. Conclusions Transcriptomic and biochemical data demonstrate a stronger impact of 1103 Paulsen rootstock than Mgt 101–14 or not grafted plants on ripening processes related to the secondary metabolite accumulations in berry skin tissue. Interestingly, the MYB14 gene, involved in the feedback regulation of resveratrol biosynthesis was up-regulated in 1103 Paulsen thus supporting a putative greater accumulation of stilbenes in mature berries.
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Affiliation(s)
- A Zombardo
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy.,Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - C Crosatti
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - P Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - L Bassolino
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.,CREA Research Centre for Cereal and Industrial Crops, via di Corticella 133, 40128, Bologna, Italy
| | - N Reshef
- French Associates institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel.,Present address: Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - S Puccioni
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy
| | - P Faccioli
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - A Tafuri
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - M Delledonne
- Department of Biotechnologies, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - A Fait
- French Associates institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - P Storchi
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy
| | - L Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - E Mica
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
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16
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Smit SJ, Vivier MA, Young PR. Comparative (Within Species) Genomics of the Vitis vinifera L. Terpene Synthase Family to Explore the Impact of Genotypic Variation Using Phased Diploid Genomes. Front Genet 2020; 11:421. [PMID: 32431727 PMCID: PMC7216305 DOI: 10.3389/fgene.2020.00421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/03/2020] [Indexed: 01/20/2023] Open
Abstract
The Vitis vinifera L. terpene synthase (VviTPS) family was comprehensively annotated on the phased diploid genomes of three closely related cultivars: Cabernet Sauvignon, Carménère and Chardonnay. VviTPS gene regions were grouped to chromosomes, with the haplotig assemblies used to identify allelic variants. Functional predictions of the VviTPS subfamilies were performed using enzyme active site phylogenies resulting in the putative identification of the initial substrate and cyclization mechanism of VviTPS enzymes. Subsequent groupings into conserved catalytic mechanisms was coupled with an analysis of cultivar-specific gene duplications, resulting in the identification of conserved and unique VviTPS clusters. These findings are presented as a collection of interactive networks where any VviTPS of interest can be queried through BLAST, allowing for a rapid identification of VviTPS-subfamily, enzyme mechanism and degree of connectivity (i.e., extent of duplication). The comparative genomic analyses presented expands our understanding of the VviTPS family and provides numerous new gene models from three diploid genomes.
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Affiliation(s)
| | | | - Philip Richard Young
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
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17
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Daldoul S, Boubakri H, Gargouri M, Mliki A. Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture. Mol Biol Rep 2020; 47:3141-3153. [PMID: 32130616 DOI: 10.1007/s11033-020-05363-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Cultivated grapevines, Vitis vinifera subsp. sativa, are thought to have been domesticated from wild populations of Vitis vinifera subsp. sylvestris in Central Asia. V. vinifera subsp. sativa is one of the most economically important fruit crops worldwide. Since cultivated grapevines are susceptible to multiple biotic and abiotic soil factors, they also need to be grafted on resistant rootstocks that are mostly developed though hybridization between American wild grapevine species (V. berlandieri, V. riparia, and V. rupestris). Therefore, wild grapevine species are essential genetic materials for viticulture to face biotic and abiotic stresses in both cultivar and rootstock parts. Actually, viticulture faces several environmental constraints that are further intensified by climate change. Recently, several reports on biotic and abiotic stresses-response in wild grapevines revealed accessions tolerant to different constraints. The emergence of advanced techniques such as omics technologies, marker-assisted selection (MAS), and functional analysis tools allowed a more detailed characterization of resistance mechanisms in these wild grapevines and suggest a number of species (V. rotundifolia, V. rupestris, V. riparia, V. berlandieri and V. amurensis) have untapped potential for new resistance traits including disease resistance loci and key tolerance genes. The present review reports on the importance of different biotechnological tools in exploring and examining wild grapevines tolerance mechanisms that can be employed to promote elite cultivated grapevines under climate change conditions.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-lif, Tunisia.
| | - Hatem Boubakri
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cedria, 2050, BP 901, Hammam-lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-lif, Tunisia
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-lif, Tunisia
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18
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Hou Y, Li H, Zhai L, Xie X, Li X, Bian S. Identification and functional characterization of the Aux/IAA gene VcIAA27 in blueberry. PLANT SIGNALING & BEHAVIOR 2019; 15:1700327. [PMID: 31822153 PMCID: PMC7012069 DOI: 10.1080/15592324.2019.1700327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 05/30/2023]
Abstract
Aux/IAA genes are an important class of players in diverse developmental processes in plants, which generally exert their functions through the auxin signaling pathway. Blueberry is an economically and nutritionally important berry-bearing crop. However, Aux/IAA genes remain unknown in blueberry. In the present study, an Aux/IAA gene (VcIAA27) was identified and characterized in blueberry, and it is most closely related to IAA27 in other plant species. Expression analysis indicated that VcIAA27 transcripts accumulate highly in shoot, flower and fruit. Interestingly, VcIAA27 was highly expressed at early fruit developmental stages, and dramatically decreased from the onset of fruit ripening, implying that VcIAA27 possibly plays important roles during fruit enlargement. Meanwhile, the analysis of promoter activity in Arabidopsis showed that strong GUS signal was detected in the trichome and hydathodes of leaves, receptacle of silique, and lateral roots of seedling. Overexpression of VcIAA27 in Arabidopsis leads to auxin-related defects such as downward-curled leaves, short or sterile siliques, shorter stature, and more shoot branches. Moreover, qPCR analysis indicated that VcIAA27 is able to alter the expression patterns of the auxin-related genes BRU6, SAG13, SAUR26 in Arabidopsis, suggesting that VcIAA27 might be negatively involved in the auxin signaling pathway. The findings will greatly contribute to future investigation of Aux/IAA-mediated mechanisms that control blueberry development, especially fruit development and ripening.
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Affiliation(s)
- Yanming Hou
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Hongxue Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, Jilin, China
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Pirrello C, Mizzotti C, Tomazetti TC, Colombo M, Bettinelli P, Prodorutti D, Peressotti E, Zulini L, Stefanini M, Angeli G, Masiero S, Welter LJ, Hausmann L, Vezzulli S. Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview. FRONTIERS IN PLANT SCIENCE 2019; 10:1394. [PMID: 31824521 PMCID: PMC6883492 DOI: 10.3389/fpls.2019.01394] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/09/2019] [Indexed: 05/23/2023]
Abstract
The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Chiara Mizzotti
- Department of Biosciences, University of Milan, Milan, Italy
| | - Tiago C. Tomazetti
- Center of Agricultural Sciences, Federal University of Santa Catarina, Rodovia Admar Gonzaga, Florianópolis, Brazil
| | - Monica Colombo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Paola Bettinelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Daniele Prodorutti
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Elisa Peressotti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Luca Zulini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Gino Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milan, Italy
| | - Leocir J. Welter
- Department of Natural and Social Sciences, Federal University of Santa Catarina, Campus of Curitibanos, Rodovia Ulysses Gaboardi, Curitibanos, Brazil
| | - Ludger Hausmann
- Julius Kühn Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
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Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development. Genomics 2019; 112:820-830. [PMID: 31136791 DOI: 10.1016/j.ygeno.2019.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/01/2019] [Accepted: 05/24/2019] [Indexed: 10/26/2022]
Abstract
Yaghooti grape of Sistan is seedless, early ripening but has compact clusters. To study gibberellin effect on cluster compactness of Yaghooti grape, it has been studied transcriptomic changes in three developmental stages (cluster formation, berry formation and final size of cluster). We found out that 5409 of 22,756 genes in cluster tissue showed significant changes under gibberellin. Finally, it was showed that 2855, 2862 and 497 genes have critically important role on above developmental stages, respectively. GO enrichment analysis showed that gibberellin enhances biochemical pathways activity. Moreover, genes involved in ribosomal structure and photosynthesis rate in cluster tissue were up- and down- regulated, respectively. In addition, we observed location of metabolomic activities was transferred from nucleus to cytoplasm and from cytoplasm to cell wall and intercellular spaces during cluster development; but there is not such situation in gibberellin treated samples.
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Affiliation(s)
- Yasoub Shiri
- Department of Agronomy and Plant Breeding, Agriculture Research Center, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia; Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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21
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Abstract
In this genome report, we describe the sequencing and annotation of the genome of the wine grape Carménère (clone 02, VCR-702). Long considered extinct, this old French wine grape variety is now cultivated mostly in Chile where it was imported in the 1850s just before the European phylloxera epidemic. Genomic DNA was sequenced using Single Molecule Real Time technology and assembled with FALCON-Unzip, a diploid-aware assembly pipeline. To optimize the contiguity and completeness of the assembly, we tested about a thousand combinations of assembly parameters, sequencing coverage, error correction and repeat masking methods. The final scaffolds provide a complete and phased representation of the diploid genome of this wine grape. Comparison of the two haplotypes revealed numerous heterozygous variants, including loss-of-function ones, some of which in genes associated with polyphenol biosynthesis. Comparisons with other publicly available grape genomes and transcriptomes showed the impact of structural variation on gene content differences between Carménère and other wine grape cultivars. Among the putative cultivar-specific genes, we identified genes potentially involved in aroma production and stress responses. The genome assembly of Carménère expands the representation of the genomic variability in grapes and will enable studies that aim to understand its distinctive organoleptic and agronomical features and assess its still elusive extant genetic variability. A genome browser for Carménère, its annotation, and an associated blast tool are available at http://cantulab.github.io/data.
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Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3 (BETHESDA, MD.) 2019; 9:755-767. [PMID: 30642874 PMCID: PMC6404599 DOI: 10.1534/g3.118.201008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
Abstract
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA
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23
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Da Silva C, Molin A, Ferrarini A, Boido E, Gaggero C, Delledonne M, Carrau F. The Tannat genome: Unravelling its unique characteristics. BIO WEB OF CONFERENCES 2019. [DOI: 10.1051/bioconf/20191201016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tannat (Vitis vinifera) is the most cultivated grapevine variety in Uruguay for the production of high quality red wines. Its berries have unusually high levels of polyphenolic compounds (anthocyanins and tannins), producing wines with intense purple colour and high antioxidant properties. Remarkably, more than 40% of its tannins are galloylated, which determines a greater antioxidant power. Technologies of massive sequencing allow the characterization of genomic variants between different clutivars. The Tannat genome was sequenced with a 134X coverage using the Illumina technology, and was annotated using transcriptomes (RNA-Seq) of different berry tissues. When comparing the genomes of Tannat with Pinot Noir PN40024 (reference genome) we found an expansion of the gene families related to the biosynthesis of polyphenols. A search base on the recently reported epicatechin galloyl transferase (ECGT) from tea leaves determined five putative genes encoding the ECGT in Tannat. Genetic analysis of one of the transcription factor that regulates the anthocyanin synthesis during berry ripening, VvMYBA1, shows the presence of Gret1 retrotransposon in one of the VvMYBA1 alleles in the Tannat clones analysed. This work makes original contributions about the molecular bases of the biosynthesis of anthocyanins and tannins during the development of the flagship grape of Uruguay.
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Ilc T, Arista G, Tavares R, Navrot N, Duchêne E, Velt A, Choulet F, Paux E, Fischer M, Nelson DR, Hugueney P, Werck-Reichhart D, Rustenholz C. Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome. PLoS One 2018; 13:e0199902. [PMID: 29953551 PMCID: PMC6023221 DOI: 10.1371/journal.pone.0199902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/15/2018] [Indexed: 12/26/2022] Open
Abstract
Cytochromes P450 are enzymes that participate in a wide range of functions in plants, from hormonal signaling and biosynthesis of structural polymers, to defense or communication with other organisms. They represent one of the largest gene/protein families in the plant kingdom. The manual annotation of cytochrome P450 genes in the genome of Vitis vinifera PN40024 revealed 579 P450 sequences, including 279 complete genes. Most of the P450 sequences in grapevine genome are organized in physical clusters, resulting from tandem or segmental duplications. Although most of these clusters are small (2 to 35, median = 3), some P450 families, such as CYP76 and CYP82, underwent multiple duplications and form large clusters of homologous sequences. Analysis of gene expression revealed highly specific expression patterns, which are often the same within the genes in large physical clusters. Some of these genes are induced upon biotic stress, which points to their role in plant defense, whereas others are specifically activated during grape berry ripening and might be responsible for the production of berry-specific metabolites, such as aroma compounds. Our work provides an exhaustive and robust annotation including clear identification, structural organization, evolutionary dynamics and expression patterns for the grapevine cytochrome P450 families, paving the way to efficient functional characterization of genes involved in grapevine defense pathways and aroma biosynthesis.
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Affiliation(s)
- Tina Ilc
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Gautier Arista
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon 1, Lyon, France
| | - Nicolas Navrot
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Eric Duchêne
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Frédéric Choulet
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Etienne Paux
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Marc Fischer
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | | | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Camille Rustenholz
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
- * E-mail:
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Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. Unraveling the transcriptional complexity of compactness in sistan grape cluster. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:198-208. [PMID: 29576073 DOI: 10.1016/j.plantsci.2018.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Yaghooti grape of Sistan is the earliest ripening grape in Iran, harvested every May annually. It is adapted to dry conditions in Sistan region and its water requirement is less than the other grape cultivars. The transcriptional complexity of this grape was studied in three stages of cluster development. Totally, 24121 genes were expressed in different cluster development steps (step 1: cluster formation, step 2: berry formation, step 3: final size of cluster) of which 3040 genes in the first stage, 2381 genes in the second stage and 2400 genes in the third stage showed a significant increase in expression. GO analysis showed that when the clusters are ripening, the activity of the nucleus, cytoplasmic, cytosol, membrane and chloroplast genes in the cluster architecture cells decreases. In contrast, the activity of the endoplasmic reticulum, vacuole and extracellular region genes enhances. When Yaghooti grape is growing and developing, some of metabolic pathways were activated in the response to biotic and abiotic stresses. Gene co-expression network reconstruction showed that AGAMOUS is a key gene in compactness of Sistan grape cluster, because it influences on expression of GA gene which leads to increase cluster length and berries size.
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Affiliation(s)
- Yasoub Shiri
- PhD student of biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, SA, Australia; School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia; Institute of Biotechnology, Shiraz University, Shiraz, Iran; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Genome-wide evolutionary characterization and expression analyses of major latex protein (MLP) family genes in Vitis vinifera. Mol Genet Genomics 2018; 293:1061-1075. [DOI: 10.1007/s00438-018-1440-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022]
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27
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Gambino G, Dal Molin A, Boccacci P, Minio A, Chitarra W, Avanzato CG, Tononi P, Perrone I, Raimondi S, Schneider A, Pezzotti M, Mannini F, Gribaudo I, Delledonne M. Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones. Sci Rep 2017; 7:17294. [PMID: 29229917 PMCID: PMC5725591 DOI: 10.1038/s41598-017-17405-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/23/2017] [Indexed: 01/27/2023] Open
Abstract
‘Nebbiolo’ (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three ‘Nebbiolo’ clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of ‘Nebbiolo’ and its intra-varietal variability useful for clonal identification were reported. In particular, several varietal transcripts identified for the first time in ‘Nebbiolo’ were disease resistance genes and single-nucleotide variants (SNVs) identified in ‘Nebbiolo’, but not in other cultivars, were associated with genes involved in the stress response. Ten newly discovered SNVs were successfully employed to identify some periclinal chimeras and to classify 98 ‘Nebbiolo’ clones in seven main genotypes, which resulted to be linked to the geographical origin of accessions. In addition, for the first time it was possible to discriminate some ‘Nebbiolo’ clones from the others.
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Affiliation(s)
- Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy.
| | | | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | | | - Paola Tononi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Stefano Raimondi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Anna Schneider
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
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28
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Harris ZN, Kovacs LG, Londo JP. RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar 'Riesling'. BMC Genomics 2017; 18:937. [PMID: 29197332 PMCID: PMC5712117 DOI: 10.1186/s12864-017-4346-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar 'Riesling' to improve annotation of the grapevine reference genome sequence. RESULTS Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.
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Affiliation(s)
- Zachary N. Harris
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
- Present address: Saint Louis University, Department of Biology, 1 N. Grand Blvd, Saint Louis, MO USA
| | - Laszlo G. Kovacs
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
| | - Jason P. Londo
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, 630 W. North Street, Geneva, NY USA
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29
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Casimiro-Soriguer CS, Muñoz-Mérida A, Pérez-Pulido AJ. Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes. Proteomics 2017; 17. [PMID: 28544705 DOI: 10.1002/pmic.201700071] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/23/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects.
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Affiliation(s)
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-JA), Universidad Pablo de Olavide, Sevilla, Spain
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30
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Yang M, Song S, Dong K, Chen X, Liu X, Rouzi M, Zhao Q, He X, Pu Y, Guan W, Ma Y, Jiang L. Skin transcriptome reveals the intrinsic molecular mechanisms underlying hair follicle cycling in Cashmere goats under natural and shortened photoperiod conditions. Sci Rep 2017; 7:13502. [PMID: 29044192 PMCID: PMC5647384 DOI: 10.1038/s41598-017-13986-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022] Open
Abstract
The growth of cashmere exhibits a seasonal pattern arising from photoperiod change. However, the underlying molecular mechanism remains unclear. We profiled the skin transcriptome of six goats at seven time points during hair follicle cycling via RNA-seq. The six goats comprised three goats exposed to a natural photoperiod and three exposed to a shortened photoperiod. During hair cycle transition, 1713 genes showed differential expression, and 332 genes showed a pattern of periodic expression. Moreover, a short photoperiod induced the hair follicle to enter anagen early, and 246 genes overlapped with the periodic genes. Among these key genes, cold-shock domain containing C2 (CSDC2) was highly expressed in the epidermis and dermis of Cashmere goat skin, although its function in hair-follicle development remains unknown. CSDC2 silencing in mouse fibroblasts resulted in the decreased mRNA expression of two key hair-follicle factors, leading to reduced cell numbers and a lower cell density. Cashmere growth or molting might be controlled by a set of periodic regulatory genes. The appropriate management of short light exposure can induce hair follicles to enter full anagen early through the activation of these regulators. The CSDC2 gene is a potentially important transcription factor in the hair growth cycle.
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Affiliation(s)
- Min Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Shen Song
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Kunzhe Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - XiaoFei Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xuexue Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Marhaba Rouzi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Qianjun Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xiaohong He
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yabin Pu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Weijun Guan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yuehui Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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Chapman B, Bellgard M. Plant Proteogenomics: Improvements to the Grapevine Genome Annotation. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/28/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Brett Chapman
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
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Matus JT, Cavallini E, Loyola R, Höll J, Finezzo L, Dal Santo S, Vialet S, Commisso M, Roman F, Schubert A, Alcalde JA, Bogs J, Ageorges A, Tornielli GB, Arce-Johnson P. A group of grapevine MYBA transcription factors located in chromosome 14 control anthocyanin synthesis in vegetative organs with different specificities compared with the berry color locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:220-236. [PMID: 28370629 DOI: 10.1111/tpj.13558] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 05/19/2023]
Abstract
Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phenotypes; however, the red pigmentation found in vegetative organs suggests the presence of additional regulators. This work describes a genomic region of chromosome 14 containing three closely related R2R3-MYB genes, named MYBA5, MYBA6 and MYBA7. Ectopic expression of the latter two genes in grapevine hairy roots promoted anthocyanin accumulation without affecting other phenylpropanoids. Transcriptomic profiling of hairy roots expressing MYBA1, MYBA6 and MYBA7 showed that these regulators share the activation of late biosynthetic and modification/transport-related genes, but differ in the activation of the FLAVONOID-3'5'-HYDROXYLASE (F3'5'H) family. An alternatively spliced MYBA6 variant was incapable of activating anthocyanin synthesis, however, because of the lack of an MYC1 interaction domain. MYBA1, MYBA6.1 and MYBA7 activated the promoters of UDP-GLUCOSE:FLAVONOID 3-O-GLUCOSYLTRANSFERASE (UFGT) and ANTHOCYANIN 3-O-GLUCOSIDE-6″-O-ACYLTRANSFERASE (3AT), but only MYBA1 induced F3'5'H in concordance with the low proportion of tri-hydroxylated anthocyanins found in MYBA6-A7 hairy roots. This putative new color locus is related to the red/cyanidic pigmentation of vegetative organs in black- and white-skinned cultivars, and forms part of the UV-B radiation response pathway orchestrated by ELONGATED HYPOCOTYL 5 (HY5). These results demonstrate the involvement of additional anthocyanin regulators in grapevine and suggest an evolutionary divergence between the two grape color loci for controlling additional targets of the flavonoid pathway.
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Affiliation(s)
- José Tomás Matus
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Erika Cavallini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Janine Höll
- Centre for Organismal Studies Heidelberg (COS Heidelberg), Im Neuenheimer Feld 360, Heidelberg, 69120, Germany
| | - Laura Finezzo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Sandrine Vialet
- INRA, UMR1083 SPO, 2 place Viala, Montpellier, F-34060, France
| | - Mauro Commisso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Federica Roman
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Largo Braccini 2, Grugliasco, 10095, Italy
| | - Andrea Schubert
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Largo Braccini 2, Grugliasco, 10095, Italy
| | - José Antonio Alcalde
- Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jochen Bogs
- Centre for Organismal Studies Heidelberg (COS Heidelberg), Im Neuenheimer Feld 360, Heidelberg, 69120, Germany
- Dienstleistungszentrum Ländlicher Raum (DLR) Rheinpfalz, Breitenweg 71, Viticulture and Enology group, Neustadt/W, D-67435, Germany
- Fachhochschule Bingen, Berlinstr. 109, Bingen am Rhein, D-55411, Germany
| | - Agnès Ageorges
- INRA, UMR1083 SPO, 2 place Viala, Montpellier, F-34060, France
| | | | - Patricio Arce-Johnson
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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Mestre P, Arista G, Piron M, Rustenholz C, Ritzenthaler C, Merdinoglu D, Chich J. Identification of a Vitis vinifera endo-β-1,3-glucanase with antimicrobial activity against Plasmopara viticola. MOLECULAR PLANT PATHOLOGY 2017; 18:708-719. [PMID: 27216084 PMCID: PMC6638254 DOI: 10.1111/mpp.12431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Inducible plant defences against pathogens are stimulated by infections and comprise several classes of pathogenesis-related (PR) proteins. Endo-β-1,3-glucanases (EGases) belong to the PR-2 class and their expression is induced by many pathogenic fungi and oomycetes, suggesting that EGases play a role in the hydrolysis of pathogen cell walls. However, reports of a direct effect of EGases on cell walls of plant pathogens are scarce. Here, we characterized three EGases from Vitis vinifera whose expression is induced during infection by Plasmopara viticola, the causal agent of downy mildew. Recombinant proteins were expressed in Escherichia coli. The enzymatic characteristics of these three enzymes were measured in vitro and in planta. A functional assay performed in vitro on germinated P. viticola spores revealed a strong anti-P. viticola activity for EGase3, which strikingly was that with the lowest in vitro catalytic efficiency. To our knowledge, this work shows, for the first time, the direct effect against downy mildew of EGases of the PR-2 family from Vitis.
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Affiliation(s)
- Pere Mestre
- SVQV, INRA, Université de StrasbourgColmarF‐68000France
| | | | | | | | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg12 rue du Général ZimmerStrasbourg67084France
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Carvalho LC, Silva M, Coito JL, Rocheta MP, Amâncio S. Design of a Custom RT-qPCR Array for Assignment of Abiotic Stress Tolerance in Traditional Portuguese Grapevine Varieties. FRONTIERS IN PLANT SCIENCE 2017; 8:1835. [PMID: 29118776 PMCID: PMC5660995 DOI: 10.3389/fpls.2017.01835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Widespread agricultural losses attributed to drought, often combined with high temperatures, frequently occur in the field, namely in Mediterranean climate areas, where the existing scenarios for climate change indicate an increase in the frequency of heat waves and severe drought events in summer. Grapevine (Vitis vinifera L.) is the most cultivated fruit species in the world and the most valuable one and is a traditional Mediterranean species. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of ancient and resilient varieties. Portugal is very rich in grapevine biodiversity, however, currently, 90% of the total producing area is planted with only 16 varieties. There is a pressing need to understand the existing genetic diversity and the physiological potential of the varieties/genotypes available to be able to respond to climate changes. With the above scenario in mind, an assembly of 65 differentially expresses genes (DEGs) previously identified as responsive to abiotic stresses in two well studied genotypes, 'Touriga Nacional' and 'Trincadeira,' was designed to scan the gene expression of leaf samples from 10 traditional Portuguese varieties growing in two regions with distinct environmental conditions. Forty-five of those DEGs proved to be associated to "abiotic stress" and were chosen to build a custom qPCR array to identify uncharacterized genotypes as sensitive or tolerant to abiotic stress. According to the experimental set-up behind the array design these DEGs can also be used as indicators of the main abiotic stress that the plant is subjected and responding to (drought, heat, or excess light).
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Minio A, Lin J, Gaut BS, Cantu D. How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes. FRONTIERS IN PLANT SCIENCE 2017; 8:826. [PMID: 28567052 PMCID: PMC5434136 DOI: 10.3389/fpls.2017.00826] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/02/2017] [Indexed: 05/23/2023]
Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Jerry Lin
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
- *Correspondence: Dario Cantu
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Wu H, Xu J, Wang J, Qin X, Wu L, Li Z, Lin S, Lin W, Zhu Q, Khan MU, Lin W. Insights into the Mechanism of Proliferation on the Special Microbes Mediated by Phenolic Acids in the Radix pseudostellariae Rhizosphere under Continuous Monoculture Regimes. FRONTIERS IN PLANT SCIENCE 2017; 8:659. [PMID: 28512464 PMCID: PMC5411758 DOI: 10.3389/fpls.2017.00659] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/11/2017] [Indexed: 05/11/2023]
Abstract
As potent allelochemicals, phenolic acids are believed to be associated with replanting disease and cause microflora shift and structural disorder in the rhizosphere soil of continuously monocultured Radix pseudostellariae. The transcriptome sequencing was used to reveal the mechanisms underlying the differential response of pathogenic bacterium Kosakonia sacchari and beneficial bacterium Bacillus pumilus on their interactions with phenolic acids, the main allelochemicals in root exudates of R. pseudostellariae in the monoculture system. The microbes were inoculated in the pots containing soil and the medicinal plant in this study. The results showed that the addition of beneficial B. pumilus to the 2-year planted soil significantly decreased the activity of soil urease, catalase, sucrase, and cellulase and increased the activity of chitinase compared with those in the 2nd-year monocropping rhizosphere soil without any treatment. However, opposite results were obtained when K. sacchari was added. Transcriptome analysis showed that vanillin enhanced glycolysis/gluconeogenesis, fatty acid biosynthesis, pentose phosphate, bacterial chemotaxis, flagellar assembly, and phosphotransferase system pathway in K. sacchari. However, protocatechuic acid, a metabolite produced by K. sacchari from vanillin, had negative effects on the citrate cycle and biosynthesis of novobiocin, phenylalanine, tyrosine, and tryptophan in B. pumilus. Concurrently, the protocatechuic acid decreased the biofilm formation of B. pumilus. These results unveiled the mechanisms how phenolic acids differentially mediate the shifts of microbial flora in rhizosphere soil, leading to the proliferation of pathogenic bacteria (i.e., K. sacchari) and the attenuation of beneficial bacteria (i.e., B. pumilus) under the monocropping system of R. pseudostellariae.
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Affiliation(s)
- Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Junjian Xu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhicheng Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Quan Zhu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad U. Khan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Wenxiong Lin,
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Rocheta M, Coito JL, Ramos MJN, Carvalho L, Becker JD, Carbonell-Bejerano P, Amâncio S. Transcriptomic comparison between two Vitis vinifera L. varieties (Trincadeira and Touriga Nacional) in abiotic stress conditions. BMC PLANT BIOLOGY 2016; 16:224. [PMID: 27733112 PMCID: PMC5062933 DOI: 10.1186/s12870-016-0911-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/28/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Predicted climate changes announce an increase of extreme environmental conditions including drought and excessive heat and light in classical viticultural regions. Thus, understanding how grapevine responds to these conditions and how different genotypes can adapt, is crucial for informed decisions on accurate viticultural actions. Global transcriptome analyses are useful for this purpose as the response to these abiotic stresses involves the interplay of complex and diverse cascades of physiological, cellular and molecular events. The main goal of the present work was to evaluate the response to diverse imposed abiotic stresses at the transcriptome level and to compare the response of two grapevine varieties with contrasting physiological trends, Trincadeira (TR) and Touriga Nacional (TN). RESULTS Leaf transcriptomic response upon heat, high light and drought treatments in growth room controlled conditions, as well as full irrigation and non-irrigation treatments in the field, was compared in TR and TN using GrapeGene GeneChips®. Breakdown of metabolism in response to all treatments was evidenced by the functional annotation of down-regulated genes. However, circa 30 % of the detected stress-responsive genes are still annotated as «Unknown» function. Selected differentially expressed genes from the GrapeGene GeneChip® were analysed by RT-qPCR in leaves of growth room plants under the combination of individual stresses and of field plants, in both varieties. The transcriptomic results correlated better with those obtained after each individual stress than with the results of plants from field conditions. CONCLUSIONS From the transcriptomic comparison between the two Portuguese grapevine varieties Trincadeira and Touriga Nacional under abiotic stress main conclusions can be drawn: 1. A different level of tolerance to stress is evidenced by a lower transcriptome reprogramming in TN than in TR. Interestingly, this lack of response in TN associates with its higher adaptation to extreme conditions including environmental conditions in a changing climate; 2. A complex interplay between stress transcriptional cascades is evidenced by antagonistic and, in lower frequency, synergistic effects on gene expression when several stresses are imposed together; 3. The grapevine responses to stress under controlled conditions are not fully extrapolated to the complex vineyard scenario and should be cautiously considered for agronomic management decision purposes.
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Affiliation(s)
- Margarida Rocheta
- Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - João L. Coito
- Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Miguel J. N. Ramos
- Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Luísa Carvalho
- Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Jörg D. Becker
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, CSIC-Universidad de La Rioja-Gobierno de la Rioja, 26007 Logroño, Spain
| | - Sara Amâncio
- Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Universidade de Lisboa, 1349-017 Lisboa, Portugal
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Dal Santo S, Commisso M, D'Incà E, Anesi A, Stocchero M, Zenoni S, Ceoldo S, Tornielli GB, Pezzotti M, Guzzo F. The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics. J Vis Exp 2016. [PMID: 27768042 DOI: 10.3791/54410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons. An untargeted LC-MS metabolomics approach is recommended due to its high sensitivity, accompanied by efficient data processing using MZmine software and a metabolite identification strategy based on fragmentation tree analysis. Comprehensive transcriptome analysis can be achieved using microarrays containing probes covering ~99% of all predicted grapevine genes, allowing the simultaneous analysis of all differentially expressed genes in the context of different terroirs. Finally, multivariate data analysis based on projection methods can be used to overcome the strong vintage-specific effect, allowing the metabolomics and transcriptomics data to be integrated and analyzed in detail to identify informative correlations.
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Affiliation(s)
| | | | | | - Andrea Anesi
- Biotechnology Department, University of Verona; Lab. of Bioorganic Chemistry, Physics Department, University of Trento
| | | | - Sara Zenoni
- Biotechnology Department, University of Verona
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Hill CB, Cassin A, Keeble-Gagnère G, Doblin MS, Bacic A, Roessner U. De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. Sci Rep 2016; 6:31558. [PMID: 27527578 PMCID: PMC4985707 DOI: 10.1038/srep31558] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/19/2016] [Indexed: 01/03/2023] Open
Abstract
Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes.
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Affiliation(s)
- Camilla Beate Hill
- School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
| | - Andrew Cassin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
| | - Gabriel Keeble-Gagnère
- School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia
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40
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Wong DCJ, Schlechter R, Vannozzi A, Höll J, Hmmam I, Bogs J, Tornielli GB, Castellarin SD, Matus JT. A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. DNA Res 2016; 23:451-466. [PMID: 27407139 PMCID: PMC5066171 DOI: 10.1093/dnares/dsw028] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023] Open
Abstract
R2R3-MYB transcription factors (TFs) belong to a large and functionally diverse protein superfamily in plants. In this study, we explore the evolution and function of this family in grapevine (Vitis vinifera L.), a high-value fruit crop. We identified and manually curated 134 genes using RNA-Seq data, and named them systematically according to the Super-Nomenclature Committee. We identified novel genes, splicing variants and grapevine/woody-specific duplicated subgroups, suggesting possible neo- and sub-functionalization events. Regulatory network analysis ascribed biological functions to uncharacterized genes and validated those of known genes (e.g. secondary cell wall biogenesis and flavonoid biosynthesis). A comprehensive analysis of different MYB binding motifs in the promoters of co-expressed genes predicted grape R2R3-MYB binding preferences and supported evidence for putative downstream targets. Enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators. Analysis of the network of Subgroup 2 showed that the resveratrol-related VviMYB14 and VviMYB15 share common co-expressed STILBENE SYNTHASE genes with the uncharacterized VviMYB13. These regulators have distinct expression patterns within organs and in response to biotic and abiotic stresses, suggesting a pivotal role of VviMYB13 in regulating stilbene accumulation in vegetative tissues and under biotic stress conditions.
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Affiliation(s)
| | | | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro, Padova, Italy
| | - Janine Höll
- Centre for Organismal Studies Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ibrahim Hmmam
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro, Padova, Italy
| | - Jochen Bogs
- Dienstleistungszentrum Laendlicher Raum Rheinpfalz, Breitenweg 71, Viticulture and Enology Group, 67435 Neustadt/W, Germany.,Fachhochschule Bingen, Berlinstr. 109, 55411 Bingen am Rhein, Germany
| | | | | | - José Tomás Matus
- Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
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Salvetti E, Campanaro S, Campedelli I, Fracchetti F, Gobbi A, Tornielli GB, Torriani S, Felis GE. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. Front Microbiol 2016; 7:937. [PMID: 27445999 PMCID: PMC4917526 DOI: 10.3389/fmicb.2016.00937] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Vitis vinifera L. cv. Corvina grape forms the basis for the production of unique wines, such as Amarone, whose distinctive sensory features are strongly linked to the post-harvest grape withering process. Indeed, this process increases sugar concentration and changes must characteristics. While microorganisms involved in must fermentation have been widely investigated, few data are available on the microbiota of withered grapes. Thus, in this paper, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortium associated with Corvina berries at the end of the withering process performed in two different conditions ("traditional withering," TW or "accelerated withering," AW), and to unveil whether changes of drying parameters could have an impact on microbial diversity. Samples of healthy undamaged berries were collected and washed, to recover microorganisms from the surface and avoid contamination with grapevine genetic material. Isolated DNA was sequenced and the data obtained were analyzed with several bioinformatics methods. The eukaryotic community was mainly composed by members of the phylum Ascomycota, including Eurotiomycetes, Sordariomycetes, and Dothideomycetes. Moreover, the distribution of the genera Aspergillus and Penicillium (class Eurotiomycetes) varied between the withered berry samples. Instead, Botryotinia, Saccharomyces, and other wine technologically useful microorganisms were relatively scarce in both samples. For prokaryotes, 25 phyla were identified, nine of which were common to both conditions. Environmental bacteria belonging to the class Gammaproteobacteria were dominant and, in particular, the TW sample was characterized by members of the family Pseudomonadaceae, while members of the family Enterobacteriaceae dominated the AW sample, in addition to Sphyngobacteria and Clostridia. Finally, the binning procedure discovered 15 putative genomes which dominated the microbial community of the two samples, and included representatives of genera Erwinia, Pantoea, Pseudomonas, Clostridium, Paenibacillus, and of orders Lactobacillales and Actinomycetales. These results provide insights into the microbial consortium of Corvina withered berries and reveal relevant variations attributable to post-harvest withering conditions, underling how WMS could open novel perspectives in the knowledge and management of the withering process of Corvina, with an impact on the winemaking of important Italian wines.
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Affiliation(s)
- Elisa Salvetti
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | | | | | - Alex Gobbi
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Sandra Torriani
- Department of Biotechnology, University of VeronaVerona, Italy
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42
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Domingos S, Fino J, Paulo OS, Oliveira CM, Goulao LF. Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 244:40-56. [PMID: 26810452 DOI: 10.1016/j.plantsci.2015.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/08/2015] [Accepted: 12/18/2015] [Indexed: 05/23/2023]
Abstract
Flower-to-fruit transition depends of nutrient availability and regulation at the molecular level by sugar and hormone signalling crosstalk. However, in most species, the identities of fruit initiation regulators and their targets are largely unknown. To ascertain the main pathways involved in stenospermocarpic table grape fruit set, comprehensive transcriptional and metabolomic analyses were conducted specifically targeting the early phase of this developmental stage in 'Thompson Seedless'. The high-throughput analyses performed disclosed the involvement of 496 differentially expressed genes and 28 differently accumulated metabolites in the sampled inflorescences. Our data show broad transcriptome reprogramming of molecule transporters, globally down-regulating gene expression, and suggest that regulation of sugar- and hormone-mediated pathways determines the downstream activation of berry development. The most affected gene was the SWEET14 sugar transporter. Hormone-related transcription changes were observed associated with increased indole-3-acetic acid, stimulation of ethylene and gibberellin metabolisms and cytokinin degradation, and regulation of MADS-box and AP2-like ethylene-responsive transcription factor expression. Secondary metabolism, the most representative biological process at transcriptome level, was predominantly repressed. The results add to the knowledge of molecular events occurring in grapevine inflorescence fruit set and provide a list of candidates, paving the way for genetic manipulation aimed at model research and plant breeding.
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Affiliation(s)
- Sara Domingos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal; BioTrop, Instituto de Investigação Científica Tropical I.P. (IICT), Lisbon, Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group, cE3c-Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c-Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Cristina M Oliveira
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal
| | - Luis F Goulao
- BioTrop, Instituto de Investigação Científica Tropical I.P. (IICT), Lisbon, Portugal.
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Pelin A, Moteshareie H, Sak B, Selman M, Naor A, Eyahpaise MÈ, Farinelli L, Golshani A, Kvac M, Corradi N. The genome of an Encephalitozoon cuniculi type III strain reveals insights into the genetic diversity and mode of reproduction of a ubiquitous vertebrate pathogen. Heredity (Edinb) 2016; 116:458-65. [PMID: 26837273 DOI: 10.1038/hdy.2016.4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023] Open
Abstract
Encephalitozoon cuniculi is a model microsporidian species with a mononucleate nucleus and a genome that has been extensively studied. To date, analyses of genome diversity have revealed the existence of four genotypes in E. cuniculi (EcI, II, III and IV). Genome sequences are available for EcI, II and III, and are all very divergent, possibly diploid and genetically homogeneous. The mechanisms that cause low genetic diversity in E. cuniculi (for example, selfing, inbreeding or a combination of both), as well as the degree of genetic variation in their natural populations, have been hard to assess because genome data have been so far gathered from laboratory-propagated strains. In this study, we aim to tackle this issue by analyzing the complete genome sequence of a natural strain of E. cuniculi isolated in 2013 from a steppe lemming. The strain belongs to the EcIII genotype and has been designated EcIII-L. The EcIII-L genome sequence harbors genomic features intermediate to known genomes of II and III lab strains, and we provide primers that differentiate the three E. cuniculi genotypes using a single PCR. Surprisingly, the EcIII-L genome is also highly homogeneous, harbors signatures of heterozygosity and also one strain-specific single-nucleotide polymorphism (SNP) that introduces a stop codon in a key meiosis gene, Spo11. Functional analyses using a heterologous system demonstrate that this SNP leads to a deficient meiosis in a model fungus. This indicates that EcIII-L meiotic machinery may be presently broken. Overall, our findings reveal previously unsuspected genome diversity in E. cuniculi, some of which appears to affect genes of primary importance for the biology of this pathogen.
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Affiliation(s)
- A Pelin
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - H Moteshareie
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - B Sak
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - M Selman
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - A Naor
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - M-È Eyahpaise
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - L Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, Plan-les-Ouates, Switzerland
| | - A Golshani
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - M Kvac
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - N Corradi
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
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44
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Andreolli M, Lampis S, Zapparoli G, Angelini E, Vallini G. Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control. Microbiol Res 2016; 183:42-52. [DOI: 10.1016/j.micres.2015.11.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/22/2015] [Indexed: 11/28/2022]
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45
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Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PLoS One 2016; 11:e0146062. [PMID: 26731733 PMCID: PMC4701411 DOI: 10.1371/journal.pone.0146062] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/11/2015] [Indexed: 12/29/2022] Open
Abstract
Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.
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Affiliation(s)
- Loren A Honaas
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Eric K Wafula
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Norman J Wickett
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Joshua P Der
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Yeting Zhang
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Naomi S Altman
- Department of Statistics, Penn State, University Park, Pennsylvania, 16802, United States of America
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - James H Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Claude W dePamphilis
- Biology Department, Penn State, University Park, Pennsylvania, 16802, United States of America
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46
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Zhang L, Ming R, Zhang J, Tao A, Fang P, Qi J. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC Genomics 2015; 16:1062. [PMID: 26666317 PMCID: PMC4678609 DOI: 10.1186/s12864-015-2256-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis. RESULTS A total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes. CONCLUSION We characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Aifen Tao
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Pingping Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jianmin Qi
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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47
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Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet RL, Schlauch KA, Haynes PA, Fait A, Cramer GR. Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. BMC Genomics 2015; 16:946. [PMID: 26573226 PMCID: PMC4647476 DOI: 10.1186/s12864-015-2115-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 10/20/2015] [Indexed: 11/23/2022] Open
Abstract
Background Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems. Results Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity (°Brix-to-titratable acidity ratio) from the same experimental vineyard. The cultivars were exposed to a mild, seasonal water-deficit treatment from fruit set until harvest in 2011. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNAseq and microarray data revealed a strong Pearson’s correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson’s correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. The mild water deficit treatment did not significantly alter the abundance of proteins or metabolites measured in the five cultivars, but did have a small effect on gene expression. Conclusions The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2115-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Steven C Van Sluyter
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - Uri Hochberg
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel.
| | - Asfaw Degu
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel.
| | - Daniel W Hopper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Richard L Tillet
- Nevada Center for Bioinformatics, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Karen A Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA. .,Nevada Center for Bioinformatics, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 84990, Israel.
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
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Wang Z, Wang B, Chen G, Jian J, Lu Y, Xu Y, Wu Z. Transcriptome analysis of the pearl oyster (Pinctada fucata) hemocytes in response to Vibrio alginolyticus infection. Gene 2015; 575:421-428. [PMID: 26363408 DOI: 10.1016/j.gene.2015.09.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 07/16/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Abstract
The pearl oyster Pinctada fucata is cultured widely for production of marine pearls in China, while mass mortalities, likely related to pathogenic infections, have occurred frequently in juvenile, mother and operated oysters. To address this issue, understanding host defense mechanisms of P. fucata against pathogenic challenge is extremely important. In the present study, a comparative analysis of hemocyte transcriptomes of P. fucata before and after Vibrio alginolyticus infection was conducted using the Illumina/Hiseq-2000 RNA-Seq technology. A total of 56,345,139 clean reads were generated and then assembled into 74,007 unigenes with an average length of 680 bp and an N50 of 1197 bp. Unigenes were annotated by comparing against non-redundant protein sequence (nr), non-redundant nucleotide (nt), Swiss-Prot, Pfam, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and 29,615 unigenes (40.01%) were annotated in at least one database. There were 636 genes (518 up-regulated and 118 down-regulated) that were significantly differentially expressed after bacterial challenge, and among which 369 were associated with 122 pathways, including classical immune-related pathways, such as 'MAPK signaling pathway', 'Chemokine signaling pathway', 'Apoptosis' and 'Wnt signaling pathway'. These findings provide information on the pearl oyster innate immunity and may contribute to developing strategies for management of diseases and long-term sustainability of P. fucata culture.
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Affiliation(s)
- Zhongliang Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Bei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Gang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Jichang Jian
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Yishan Lu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China
| | - Youhou Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou 535099, China
| | - Zaohe Wu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524025, China; Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Amrine KCH, Blanco-Ulate B, Riaz S, Pap D, Jones L, Figueroa-Balderas R, Walker MA, Cantu D. Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew. HORTICULTURE RESEARCH 2015; 2:15037. [PMID: 26504579 PMCID: PMC4591678 DOI: 10.1038/hortres.2015.37] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 05/24/2023]
Abstract
Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study, we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions 'Karadzhandahal', DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.
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Affiliation(s)
- Katherine C H Amrine
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dániel Pap
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - Laura Jones
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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Yang M, Zhu L, Pan C, Xu L, Liu Y, Ke W, Yang P. Transcriptomic Analysis of the Regulation of Rhizome Formation in Temperate and Tropical Lotus (Nelumbo nucifera). Sci Rep 2015; 5:13059. [PMID: 26279185 PMCID: PMC4538393 DOI: 10.1038/srep13059] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 07/10/2015] [Indexed: 12/21/2022] Open
Abstract
Rhizome is the storage organ of lotus derived from modified stems. The development of rhizome is a complex process and depends on the balanced expression of the genes that is controlled by environmental and endogenous factors. However, little is known about the mechanism that regulates rhizome girth enlargement. In this study, using RNA-seq, transcriptomic analyses were performed at three rhizome developmental stages-the stolon, middle swelling and later swelling stage -in the cultivars 'ZO' (temperate lotus with enlarged rhizome) and 'RL' (tropical lotus with stolon). About 348 million high-quality reads were generated, and 88.5% of the data were mapped to the reference genome. Of 26783 genes identified, 24069 genes were previously predicted in the reference, and 2714 genes were novel transcripts. Moreover, 8821 genes were differentially expressed between the cultivars at the three stages. Functional analysis identified that these genes were significantly enriched in pathways carbohydrate metabolism and plant hormone signal transduction. Twenty-two genes involved in photoperiod pathway, starch metabolism and hormone signal transduction were candidate genes inducing rhizome girth enlargement. Comparative transcriptomic analysis detected several differentially expressed genes and potential candidate genes required for rhizome girth enlargement, which lay a foundation for future studies on molecular mechanisms underlying rhizome formation.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Lingping Zhu
- 1] Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Pan
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Liming Xu
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Weidong Ke
- National Garden of Aquatic Vegetable, Wuhan Institute of Vegetable Science, Wuhan 430065, Hubei, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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