A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening

Cramer, Grant R.; Cochetel, No eacute; Ghan, Ryan; Destrac-Irvine, Agnès; Delrot, Serge

doi:10.1101/729236

Cited by 2 publications

(2 citation statements)

References 117 publications

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“…Expression of the dicistronic genes and dicistronic tRNA was assessed by plotting their expression values against the distribution of the total gene expression for each tissue from the RNA-seq data. Gene annotation for dicistronic genes was obtained from EnsemblPlants release 45 (http://plants.ensembl.org/Vitis_vinifera/Info/Index), BLASTP search from NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi), from the grapevine V1 annotation of PN40024 (Jaillon et al 2007) and from the Additional file 1 of Cramer et al (2020). Protein information and gene ontology terms were obtained from UniProt (https://www.uniprot.org/uniprot).…”

Section: Methodsmentioning

confidence: 99%

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Fabres

Sai

Pederson

et al. 2020

Preprint

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Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures can also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include the expression of non-coding RNA species such as small nucleolar RNAs and microRNA clusters. It is not known, however, the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors contributing to their expression. To address these questions, we analysed tRNA-mRNA dicistronic transcripts in the major horticultural crop grapevine (Vitis vinifera) using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA sequencing data. We identified dicistronic tRNA-mRNA in grapevine leaf and berry samples from 22 commercial vineyards covering six sub-regions of the Barossa wine growing region, Australia. Of the 124 tRNA genes that were expressed in both tissues, 18 tRNA were expressed forming part of 19 dicistronic tRNA-mRNA molecules. The presence and the abundance of dicistronic molecules was tissue and geographic sub-region specific. In leaf tissue, the expression patterns of dicistronic tRNA-mRNAs significantly correlated with tRNA expression, suggesting that transcriptional regulation of their expression might be linked. We also found evidence of evolutionary conservation of dicistronic candidates in grapevine, and previously reported dicistronic transcripts in Arabidopsis, indicating a syntenic genomic arrangement of tRNAs and protein coding genes between species.

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Section: Methodsmentioning

confidence: 99%

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Fabres

Sai

Pederson

et al. 2020

Preprint

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“…Transcriptomics approaches have become frequently employed in grapevine physiological studies focusing either on berry development or on responses to abiotic or biotic stresses. Several developmental studies targeted the incipit of berry ripening 6,7 or the late phases of berry development [8][9][10][11] for finding master regulators of key transitions 12 . However, albeit the clustering of RNA-seq samples largely depended on sugar concentrations, in none of these works, there was a hint on the origin of the arrest of sugar phloem unloading in the ripening berry.…”

Section: Introductionmentioning

confidence: 99%

Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit

Savoi¹,

Torregrosa²,

Romieu³

2021

Hortic Res

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Transcriptomic changes at the cessation of sugar accumulation in the pericarp of Vitis vinifera were addressed on single berries re-synchronised according to their individual growth patterns. The net rates of water, sugars and K+ accumulation inferred from individual growth and solute concentration confirmed that these inflows stopped simultaneously in the ripe berry, while the small amount of malic acid remaining at this stage was still being oxidised at low rate. Re-synchronised individual berries displayed negligible variations in gene expression among triplicates. RNA-seq studies revealed sharp reprogramming of cell-wall enzymes and structural proteins at the stop of phloem unloading, associated with an 80% repression of multiple sugar transporters and aquaporins on the plasma or tonoplast membranes, with the noticeable exception of H+/sugar symporters, which were rather weakly and constitutively expressed. This was verified in three genotypes placed in contrasted thermo-hydric conditions. The prevalence of SWEET suggests that electrogenic transporters would play a minor role on the plasma membranes of SE/CC complex and the one of the flesh, while sucrose/H+ exchangers dominate on its tonoplast. Cis-regulatory elements present in their promoters allowed to sort these transporters in different groups, also including specific TIPs and PIPs paralogs, and cohorts of cell wall-related genes. Together with simple thermodynamic considerations, these results lead to propose that H+/sugar exchangers at the tonoplast, associated with a considerably acidic vacuolar pH, may exhaust cytosolic sugars in the flesh and alleviate the need for supplementary energisation of sugar transport at the plasma membrane.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening

Abstract: 1 Background 2

Cited by 2 publications

References 117 publications

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit

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