scholarly journals Iso-Seq allows genome-independent transcriptome profiling of grape berry development

2018 ◽  
Author(s):  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Rosa Figueroa-Balderas ◽  
Amanda M. Vondras ◽  
Barbara Blanco-Ulate ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcriptional Profiling ◽  
Transcriptome Profiling ◽  
Grape Berry ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Grape Berries ◽  
Gene Space ◽  
A Genome ◽  
Computationally Intensive

AbstractTranscriptomics 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 (Iso-Seq) to sequence full-length cDNA and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, Illumina 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.

Compositional Changes During Grape Berry Development in Relation to Abscisic Acid and Salinity

1978 ◽  
Vol 5 (4) ◽  
pp. 415 ◽  
Author(s):  
WJS Downton ◽  
BR Loveys
Keyword(s):  
Abscisic Acid ◽  
Chemical Composition ◽  
Grape Berry ◽  
Reducing Sugar ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Grape Berries ◽  
Low Salt ◽  
Compositional Changes

Changes in the chemical composition of developing Cabernet Sauvignon berries from salt-treated and low-salt vines were followed. Although salinity advanced the timing of veraison, the sequence of changes in the salt-affected berries remained the same as in berries from control plants, viz. concentrations of abscisic acid and reducing sugar increased before proline, arginine, potassium and chloride increased, and before acidity declined. The contribution of these substances to osmotic changes within developing grape berries is discussed.

scholarly journals Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

2021 ◽  
Author(s):  
Noé Cochetel ◽  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Amanda M Vondras ◽  
Rosa Figueroa-Balderas ◽  
...  
Keyword(s):  
Single Molecule ◽  
Interleukin 1 ◽  
Plasmopara Viticola ◽  
Cabernet Sauvignon ◽  
Disease Resistance Gene ◽  
Chromosome Fusion ◽  
Protein Coding ◽  
Downy Mildews ◽  
A Genome ◽  
Muscadinia Rotundifolia

Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at .www.grapegenomics.com

scholarly journals Influence of Light on Grape Berry Growth and Composition Varies during Fruit Development

1996 ◽  
Vol 121 (5) ◽  
pp. 869-874 ◽  
Author(s):  
N.K. Dokoozlian ◽  
W.M. Kliewer
Keyword(s):  
Fruit Development ◽  
Light Exposure ◽  
Grape Berry ◽  
Pinot Noir ◽  
Stage Iii ◽  
Cabernet Sauvignon ◽  
Fruit Softening ◽  
Berry Development ◽  
Development Stages ◽  
Final Sample

Potted `Cabernet Sauvignon' and `Pinot noir' grapevines (Vitis vinifera L.) grown in a sunlit phytotron were used to study the influence of cluster light exposure during various stages of fruit development on berry growth and composition. Clusters grown without light during berry development stages I and II, stage III, or stages I, II, and III, were compared to clusters exposed to light throughout fruit development (control). The temperature of light-exposed and nonexposed fruit was similar. The weights and diameters of berries grown without light during stages I and II, or stages I, II, and III, were similar and significantly lower than those of the control. Fruit softening in both cultivars, as well as the initiation of berry coloration, was delayed when berries were grown without light during stages I and II. Following fruit softening, berries grown without light during stages I, II, and III were lower in sugar than the control. On the final sample date, `Cabernet Sauvignon' berries grown without light during stages I, II, and III were higher in malate compared to the control. `Pinot noir' berries grown without light during stages I and II, or stages I, II, and III, were lower in malate before fruit softening, and higher in malate following fruit softening, than the control. Control berries had greater skin anthocyanins and phenolics compared to the remaining treatments. Berries grown without light during stages I and II, or stage III, were greater in anthocyanins and phenolics than fruit grown without light during stages I, II, and III. Light had no effect on fruit tartrate concentration or juice pH. Light had its greatest impact on fruit development during the initial stages of berry growth. Berry growth was reduced and ripening delayed when fruit were grown without light during stages I and II. Normal fruit development was not fully restored when these fruit were exposed to light during stage III.

scholarly journals Towards the definition of a detailed transcriptomic map of berry development

2019 ◽  
Vol 13 ◽  
pp. 01001
Author(s):  
Marianna Fasoli ◽  
Chandra L. Richter ◽  
Sara Zenoni ◽  
Marco Sandri ◽  
Paola Zuccolotto ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Grape Berry ◽  
Pinot Noir ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Rna Seq ◽  
Molecular Events ◽  
Molecular Information ◽  
Definition Of ◽  
Transcriptomic Level

The progress of the grapevine genomics and the development of high-throughput technologies for gene expression analysis stimulated the investigation of the physical, biochemical and physiological changes of grape berry growth and maturation at transcriptomic level. The molecular information generated in the last decade is however still fragmented since it relies upon detailed analysis of few stages and thus lacks continuity over grape development. To identify the molecular events associated with berry development at a higher temporal resolution and define a transcriptomic map, we performed RNA-seq analysis of berry samples collected every week from fruit-set to maturity in Pinot noir and Cabernet Sauvignon for three consecutive years, resulting in 219 samples. Using the most variable portion of the transcriptome, we built a preliminary transcriptomic model of berry development based on the Cabernet Sauvignon samples. The Pinot noir samples were then aligned onto this preliminary ripening map to investigate its performance in describing the development of another grape variety. A further step for testing the model was the projection of RNA-seq samples of fruit development of five red-skin Italian cultivars. For all these surveys, the transcriptomic route allowed a precise definition of the progression of berry development during both formation and ripening phases.

Firmness and grape berry maturation. Definition of different rheological parameters during the ripening

OENO One ◽  
1997 ◽  
Vol 31 (3) ◽  
pp. 127 ◽  
Author(s):  
Jean-Pierre Robin ◽  
Philippe Abbal ◽  
Jean-Michel Salmon
Keyword(s):  
Mechanical Properties ◽  
Mechanical Behaviour ◽  
Grape Berry ◽  
Rheological Parameters ◽  
Berry Development ◽  
Elasticity Coefficient ◽  
Grape Berries ◽  
Definition Of ◽  
Flat Tool ◽  
Berry Maturation

<p style="text-align: justify;">Mechanical properties of Shiraz and Gamay grape berries were studied in relation with their maturity state using the Penelaup<sup>TM</sup> rheometer. The analysis of the constrains registered during berry crushing with the flat tool of the device, up to the pellicular tearing, allowed the definition of different rheological parameters and the characterisation of mechanical behaviour of grape and its evolution with the degree of ripening. The analysis of the deformability curves shows, independently of the cultivar, that berry behaviour is not elastical except for some berries at the beginning and at the end of the ripening. This behaviour can be characterised by two indexes expressing the curvature sense of deformability curves, the curvature degree in a way reflecting the turgescence state of the grape. Berry firmness was also considered in two different ways: the initial firmness which represents the elasticity coefficient of the fruit at the beginning of the deformation, and the bursting firmness which can be considered as the pellicular elasticity coefficient. Others parameters, as the pellicular strength which can be expressed from the value of the displacement at berry bursting and the energy used for the deformation were also defined. The evolution of these different parameters during ripening confirms that berry softening at the véraison time depends on the cultivar and on environmental conditions as the vintage. The analysis of the evolutions also indicates that pellicular strength is maximum at this crucial period of berry development.</p>

scholarly journals Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 429 ◽  
Author(s):  
Laurent G Deluc ◽  
Jérôme Grimplet ◽  
Matthew D Wheatley ◽  
Richard L Tillett ◽  
David R Quilici ◽  
...  
Keyword(s):  
Grape Berry ◽  
Cabernet Sauvignon ◽  
Berry Development

scholarly journals Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

2019 ◽  
pp. g3.201008.2018 ◽  
Author(s):  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Rosa Figueroa-Balderas ◽  
Amanda M. Vondras ◽  
Barbara Blanco-Ulate ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Grape Berry ◽  
Berry Development

scholarly journals Combined Metabolite and Transcriptome Profiling Reveals the Norisoprenoid Responses in Grape Berries to Abscisic Acid and Synthetic Auxin

2021 ◽  
Vol 22 (3) ◽  
pp. 1420
Author(s):  
Lei He ◽  
Nan Meng ◽  
Simone D. Castellarin ◽  
Yu Wang ◽  
Qi Sun ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Posttranscriptional Regulation ◽  
Affinity Purification ◽  
Transcriptome Profiling ◽  
Grape Berry ◽  
Vitis Vinifera L ◽  
Naphthaleneacetic Acid ◽  
Synthetic Auxin ◽  
Grape Berries ◽  
Positive Effects

The abscisic acid (ABA) increase and auxin decline are both indicators of ripening initiation in grape berry, and norisoprenoid accumulation also starts at around the onset of ripening. However, the relationship between ABA, auxin, and norisoprenoids remains largely unknown, especially at the transcriptome level. To investigate the transcriptional and posttranscriptional regulation of the ABA and synthetic auxin 1-naphthaleneacetic acid (NAA) on norisoprenoid production, we performed time-series GC-MS and RNA-seq analyses on Vitis vinifera L. cv. Cabernet Sauvignon grape berries from pre-veraison to ripening. Higher levels of free norisoprenoids were found in ABA-treated mature berries in two consecutive seasons, and both free and total norisoprenoids were significantly increased by NAA in one season. The expression pattern of known norisoprenoid-associated genes in all samples and the up-regulation of specific alternative splicing isoforms of VviDXS and VviCRTISO in NAA-treated berries were predicted to contribute to the norisoprenoid accumulation in ABA and NAA-treated berries. Combined weighted gene co-expression network analysis (WGCNA) and DNA affinity purification sequencing (DAP-seq) analysis suggested that VviGATA26, and the previously identified switch genes of myb RADIALIS (VIT_207s0005g02730) and MAD-box (VIT_213s0158g00100) could be potential regulators of norisoprenoid accumulation. The positive effects of ABA on free norisoprenoids and NAA on total norisoprenoid accumulation were revealed in the commercially ripening berries. Since the endogenous ABA and auxin are sensitive to environmental factors, this finding provides new insights to develop viticultural practices for managing norisoprenoids in vineyards in response to changing climates.

scholarly journals Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

2020 ◽  
Author(s):  
Noe Cochetel ◽  
Andrea Minio ◽  
Amanda Vondras ◽  
Rosa Figueroa-Balderas ◽  
Dario Cantu
Keyword(s):  
Single Molecule ◽  
Interleukin 1 ◽  
Plasmopara Viticola ◽  
Cabernet Sauvignon ◽  
Disease Resistance Gene ◽  
Chromosome Fusion ◽  
Protein Coding ◽  
Downy Mildews ◽  
A Genome ◽  
Muscadinia Rotundifolia

Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at www.grapegenomics.com.

scholarly journals Characterization and Action Mechanism Analysis of VvmiR156b/c/d-VvSPL9 Module Responding to Multiple-Hormone Signals in the Modulation of Grape Berry Color Formation

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 896
Author(s):  
Ziwen Su ◽  
Xicheng Wang ◽  
Xuxian Xuan ◽  
Zilu Sheng ◽  
Haoran Jia ◽  
...  
Keyword(s):  
Color Change ◽  
Grape Berry ◽  
Anthocyanin Synthesis ◽  
Structural Genes ◽  
Expression Levels ◽  
Color Formation ◽  
Grape Berries ◽  
Ripening Stages ◽  
Color Conversion ◽  
Hormone Signals

In recent years, more and more reports have shown that the miR156-SPL module can participate in the regulation of anthocyanin synthesis in plants. However, little is known about how this module responds to hormonal signals manipulating this process in grapes. In this study, exogenous GA, ABA, MeJA, and NAA were used to treat the ‘Wink’ grape berries before color conversion, anthocyanin and other related quality physiological indexes (such as sugar, aroma) were determined, and spatio-temporal expression patterns of related genes were analyzed. The results showed that the expression levels of VvmiR156b/c/d showed a gradually rising trend with the ripening and color formation of grape berries, and the highest expression levels were detected at day 28 after treatment, while the expression level of VvSPL9 exhibited an opposite trend as a whole, which further verifies that VvmiR156b/c/d can negatively regulate VvSPL9. Besides, VvmiR156b/c/d was positively correlated with anthocyanin content and related genes levels, while the expression pattern of VvSPL9 showed a negative correlation. Analysis of promoter cis-elements and GUS staining showed that VvmiR156b/c/d contained a large number of hormone response cis-elements (ABA, GA, SA, MeJA, and NAA) and were involved in hormone regulation. Exogenous ABA and MeJA treatments significantly upregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early stage of color conversion and made grape berries quickly colored. Interestingly, GA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early color-change period, but significantly upregulated in the middle color-change and ripening stages, therefore GA mainly modulated grape berry coloring in the middle- and late-ripening stages. Furthermore, NAA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes and delayed the peak expression of genes. Meanwhile, to further recognize the potential functions of VvmiR156b/c/d, the mature tomato transient trangenetic system was utilized in this work. Results showed that transient overexpression of VvmiR156b/c/d in tomato promoted fruit coloring and overexpression of VvSPL9 inhibited fruit coloration. Finally, a regulatory network of the VvmiR156b/c/d-VvSPL9 module responsive to hormones modulating anthocyanin synthesis was developed. In conclusion, VvmiR156b/c/d-mediated VvSPL9 participated in the formation of grape color in response to multi-hormone signals.

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