27 research outputs found
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The genomic diversification of grapevine clones.
BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome
Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling.
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Developmental differences in Vitis vinifera berries and the impact of GLRaV3 on the transcriptome during ripening
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. Next-generation sequencing.xlsx
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. miRNA Hairpins.pdf
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. Differentially abundant sRNA and targets.xlsx
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. miRNA targets.txt
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. DCeN scores.xlsx
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways
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Supplemental File. miRNA Hairpin Key and Annotation.xlsx
In the study of any developmental process, whether in plants, animals, or other models, it is prudent to consider the developmental position of the subjects being measured. This is generally not taken into consideration in grapevine studies despite a growing body of literature documenting that fruits within clusters develop and ripen non-uniformly. What complicates such accounting is that grape berries develop and ripen within a complex, extensively branched panicle. In the studies that follow, a tagging strategy was deployed in which fruits were labeled on their dates of anthesis or developmental position at véraison (when 50% of a cluster has initiated ripening) and subsequently sampled. Using this approach, why fruits initiate ripening unevenly and how much variation persists late in the ripening process were explored. The ripening onset for individual berries and the hormonal shifts characteristic of the ripening onset were best associated with their seed content, with flowering time playing an inconsistent and small role. Late in ripening, the abundance of enologically meaningful metabolites were still able to distinguish berries based on their developmental position at véraison.Grape Leafroll-associated Virus 3 (GLRaV3) is the most consequential virus that affects grapevine globally, with reports showing infected vines yield less and produce poorer quality fruit. Furthermore, GLRaV3 is reported to affect grapevines in a developmentally specific way. Given the developmental heterogeneity within clusters and that viral symptoms in the fruit occur in a developmentally-sensitive manner, the aforementioned tagging strategy was used to study the impact of GLRaV3 in berries during ripening. RNA sequencing and small RNA sequencing libraries were constructed to capture transcriptome-wide changes in gene expression, small RNAs, and the production of viral small interfering RNAs, as well as to identify novel micro and other small RNAs abundant during ripening and affected by GLRaV3. The effects of GLRaV3 in terms of gene expression and small RNA abundance were most numerous at véraison and included ordered and disordered responses. Most modules of co-expressed genes exhibited ordered responses, with groups of genes becoming differentially expressed while remaining co-expressed. However, disordered responses were observed as well. Various regulatory strategies were indicted in the orchestration of GLRaV3 responses, as were genes involved in the crosstalk between metabolite biosynthetic pathways and hormone signaling pathways