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Gene prediction workflow. (A) RNAseq samples are aligned on the reference genome. (B) Biological replicate alignments are merged together into 64 different datasets. Transcript reconstruction was performed independently on each dataset using three different programs: Cufflinks, Scripture and Isolasso. The Venn diagram shows the percentage of reconstructed transcripts in common among the three software while the numbers between brackets indicates the average number of reconstructed transcripts per sample. We selected only those transcript models predicted by at least two programs and with a length higher than 150 bases. (C) The selected transcripts were assembled using PASA software. (D) PASA assemblies were used to update v1 gene predictions. (E) A new gene prediction was performed integrating with EvidenceModeler (EVM) software different sources of evidence such as PASA transcripts, ESTs and proteins alignments and Augustus prediction trained with PASA assemblies. The produced gene set was compared to v1 gene prediction and only the new gene loci were selected for further analysis. After applying different filtering criteria, we obtained a final dataset of 2,258 new genes. (F) The final v2 gene prediction integrates genes generated by the steps described in D (v1 update) and E (new gene prediction).
Source publication
Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes.
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Purpose
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Citations
... assembly was achieved using hisat2 with default settings and the -sensitive option (Kim et al. 2015). This is followed by gene count summarization using FeatureCounts (Liao et al. 2014) and the CRIBI V2 prediction (Vitulo et al. 2014) as described previously. Using edgeR (Robinson et al. 2010) with the quasi-likelihood F-test method in R (https://cran.r-project.org/), ...
Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix–loop–helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively. Transcriptome analysis of VvbHLH036-overexpressed roots identified threonine synthase (VvThrC1) as a potential downstream target of VvbHLH036. We confirmed that VvbHLH036 could bind the VvThrC1 promoter and activate its expression. Both the transcripts of VvThrC1 and the content of threonine were significantly induced in the leaves and roots of grapevine under cold treatment compared to controls. Conversely, these dynamics were significantly suppressed in the roots of CRISPR/Cas9-induced knockout of VvbHLH036. These observations support the regulation of threonine accumulation by VvbHLH036 through VvThrC1 during cold stress in grapevine. Furthermore, overexpression and CRISPR/Cas9-mediated knockout of VvThrC1 also confirmed its role in regulating threonine content and cold tolerance in transgenic roots at low temperature. Exogenous threonine treatment increased cold tolerance and reduced the accumulation of superoxide anions and hydrogen peroxide in grapevine leaves. Together, these findings point to the pivotal role of VvbHLH036 and VvThrC1 in the cold stress response in grapes by regulating threonine biosynthesis.
... Transcriptome data analysis has revealed that at least 44 (12.4%) of 354 high-confidence miRNA binding sites in Arabidopsis are affected by AS (Yang et al. 2012). (Vitulo et al. 2014) Research suggests that this process may also play a role in plant responses to osmotic adjustment, including drought, as indicated by the 139 grapevine genes with miRNA target sites affected by AS. AS events have been observed in both grape (Mica et al. 2010) and Arabidopsis (Hirsch et al. 2006), indicating an additional level of regulatory control over miRNAtargeted genes. ...
Impact of elevated temperatures on the genetic
and morpho‑physiological traits of cotton
... Transcriptome data analysis has revealed that at least 44 (12.4%) of 354 high-confidence miRNA binding sites in Arabidopsis are affected by AS (Yang et al. 2012). (Vitulo et al. 2014) Research suggests that this process may also play a role in plant responses to osmotic adjustment, including drought, as indicated by the 139 grapevine genes with miRNA target sites affected by AS. AS events have been observed in both grape (Mica et al. 2010) and Arabidopsis (Hirsch et al. 2006), indicating an additional level of regulatory control over miRNAtargeted genes. ...
... Transcriptome data analysis has revealed that at least 44 (12.4%) of 354 high-confidence miRNA binding sites in Arabidopsis are affected by AS (Yang et al. 2012). (Vitulo et al. 2014) Research suggests that this process may also play a role in plant responses to osmotic adjustment, including drought, as indicated by the 139 grapevine genes with miRNA target sites affected by AS. AS events have been observed in both grape (Mica et al. 2010) and Arabidopsis (Hirsch et al. 2006), indicating an additional level of regulatory control over miRNAtargeted genes. ...
... Transcriptome data analysis has revealed that at least 44 (12.4%) of 354 high-confidence miRNA binding sites in Arabidopsis are affected by AS (Yang et al. 2012). (Vitulo et al. 2014) Research suggests that this process may also play a role in plant responses to osmotic adjustment, including drought, as indicated by the 139 grapevine genes with miRNA target sites affected by AS. AS events have been observed in both grape (Mica et al. 2010) and Arabidopsis (Hirsch et al. 2006), indicating an additional level of regulatory control over miRNAtargeted genes. ...
Heat stress poses a significant threat to cotton, affecting crucial developmental stages from fertilization to boll development and thereby reducing both yield and quality. As global climate change advances, the likelihood of severe heat waves increases, presenting a serious challenge to agricultural production and our ability to feed a growing population. Cotton’s resilience to heat involves a suite of physiological and biochemical responses, including adjustments in water management and protective mechanisms at the cellular level, such as the synthesis of heat shock proteins (HSPs) and antioxidants. These adaptations are crucial for maintaining cellular integrity and overall plant health under thermal stress. Recent research highlighted specific proteins and enzymes within the plant that help combat stress related damage. However, the exact molecular mechanisms facilitating these protective responses are not fully delineated. Further research is needed to identify and validate additional molecular mechanisms
... Transcriptome data analysis has revealed that at least 44 (12.4%) of 354 high-confidence miRNA binding sites in Arabidopsis are affected by AS (Yang et al. 2012). (Vitulo et al. 2014) Research suggests that this process may also play a role in plant responses to osmotic adjustment, including drought, as indicated by the 139 grapevine genes with miRNA target sites affected by AS. AS events have been observed in both grape (Mica et al. 2010) and Arabidopsis (Hirsch et al. 2006), indicating an additional level of regulatory control over miRNAtargeted genes. ...
Heat stress poses a significant threat to cotton, affecting crucial developmental stages from fertilization to boll development and thereby reducing both yield and quality. As global climate change advances, the likelihood of severe heat waves increases, presenting a serious challenge to agricultural production and our ability to feed a growing population. Cotton’s resilience to heat involves a suite of physiological and biochemical responses, including adjustments in water management and protective mechanisms at the cellular level, such as the synthesis of heat shock proteins (HSPs) and antioxidants. These adaptations are crucial for maintaining cellular integrity and overall plant health under thermal stress. Recent research highlighted specific proteins and enzymes within the plant that help combat stress-related damage. However, the exact molecular mechanisms facilitating these protective responses are not fully delineated. Further research is needed to identify and validate additional molecular mechanisms underlying the plant’s response to heat stress. Additionally, exploring new breeding strategies for the development of more resilient cultivars. In addition, field trials and testing under real-world conditions will be essential to assess the effectiveness of the proposed strategies for mitigating the negative effects of heat stress on crop yields.
... connected. Among those relevant to the experiments of this article, drops in cell turgor 79 precede berry softening, which is reflected by lower elasticity 16 . Berry softening is operated on 80 an individual berry basis. ...
Understanding ripening patterns and governing ripening speed are central aspects of grapevine ( Vitis vinifera ) berry biology owing to the importance of grape ripeness in winemaking. Despite this, the genetic control of ripening is largely unknown. Here, we report a major quantitative trait locus that controls ripening speed, expressed as speed of sugar accumulation. A haplotype originating from the species Vitis riparia halves maximum speed regardless of crop levels and berry sizes. The sequence of events that are normally completed at the onset of ripening in a two-week period known in viticulture as veraison are taking place at a slower speed, thereby attaining ripeness under milder weather conditions in late summer. V. vinifera cultivars show limited phenotypic variation for ripening speed and no selective sweep in the causal genomic region that could derive from domestication or improvement. Closely related species make up for the lack of standing variation, supplying major effect alleles for adapting grape cultivars to climate change.
HIGHLIGHT / SIGNIFICANCE STATEMENT
Reducing the speed of fruit ripening genetically is a means for adapting the grape berry developmental program to the changing needs of the wine industry and in response to global warming. We identified a haplotype in a wild grape species that slows down the speed of ripening in progenies of Vitis vinifera by limiting the speed of sugar accumulation throughout the duration of ripening, a condition of great importance for winemakers to harvest their grapes at the desired level of technological ripeness.
... Flowering plants possess a significant number of SR proteins, with Arabidopsis having 18 members [29], Brachypodium [17,30], rice [24,31], and grape (Vitis vinifera) [18,32]. In Arabidopsis, several sequence-conserved splicing factors and regulators have been ...
... Flowering plants possess a significant number of SR proteins, with Arabidopsis having 18 members [29], Brachypodium [17,30], rice [24,31], and grape (Vitis vinifera) [18,32]. In Arabidopsis, several sequence-conserved splicing factors and regulators have been functionally characterized, playing crucial roles in regulating various aspects of development and stress responses [33,34]. ...
Internode length is a crucial phenotypic trait of bamboo, significantly impacting its processing and utilization. Phyllostachys edulis ‘Tubaeformis’ (Shengyin Bamboo), a variety of Moso bamboo, exhibits drastically shortened internodes, making it a valuable ornamental bamboo species. We used PacBio single-molecule long-read sequencing and second-generation sequencing to identify genome-wide alternative splicing (AS) events in Moso bamboo and its dwarf mutant, Shengyin bamboo, and compared the differences between the two. Our sequencing data unveiled 139,539 AS events, with retained introns as the most prevalent events. A large number of genes were differentially alternatively spliced (DAS) between Moso bamboo and Shengyin bamboo, and genes related to RNA splicing were most significantly enriched. The high expression of SR isoforms in the 24th internode of Moso bamboo is likely the main factor leading to its greater number of alternative splicing events. Alternative splicing affects the functional domains of partial GRF, E2F, and NAMisoforms, leading to the loss of domains in some isoforms and enabling some isoforms to acquire new functional domains, and this phenomenon is more common in Shengyin bamboo. AS modifies the functional domains of certain GRF isoforms, frequently resulting in domain losses or endowing isoforms with novel domains, and this phenomenon is more common in Shengyin bamboo. We used PacBio single-molecule long-read sequencing and second-generation sequencing to identify genome-wide alternative splicing (AS) events in Moso bamboo and its dwarf mutant, Shengyin Bamboo and compared the differences between the two.
... On the other hand, RI event was reported to be the most frequent event induced by salt stress in Arabidiopsis (Ding et al., 2014b), wheat , cotton (Zhu et al., 2018) and Barley (Fu et al., 2019), while A3SS was the mostly affected AS events in rice by salt stress (Fu et al., 2019). Given that the differences in AS profiles are related to tissue type, stress condition and genotype (Gan et al., 2011;Vitulo et al., 2014;Martıń et al., 2021;Zhou et al., 2022), the differences on the alternative splicing preference induced by salt may contribute to the evolutionary adaptation process in tomato. ...
Salt stress is one of the dominant abiotic stress conditions that cause severe damage to plant growth and, in turn, limiting crop productivity. It is therefore crucial to understand the molecular mechanism underlying plant root responses to high salinity as such knowledge will aid in efforts to develop salt-tolerant crops. Alternative splicing (AS) of precursor RNA is one of the important RNA processing steps that regulate gene expression and proteome diversity, and, consequently, many physiological and biochemical processes in plants, including responses to abiotic stresses like salt stress. In the current study, we utilized high-throughput RNA-sequencing to analyze the changes in the transcriptome and characterize AS landscape during the early response of tomato root to salt stress. Under salt stress conditions, 10,588 genes were found to be differentially expressed, including those involved in hormone signaling transduction, amino acid metabolism, and cell cycle regulation. More than 700 transcription factors (TFs), including members of the MYB, bHLH, and WRKY families, potentially regulated tomato root response to salt stress. AS events were found to be greatly enhanced under salt stress, where exon skipping was the most prevalent event. There were 3709 genes identified as differentially alternatively spliced (DAS), the most prominent of which were serine/threonine protein kinase, pentatricopeptide repeat (PPR)-containing protein, E3 ubiquitin-protein ligase. More than 100 DEGs were implicated in splicing and spliceosome assembly, which may regulate salt-responsive AS events in tomato roots. This study uncovers the stimulation of AS during tomato root response to salt stress and provides a valuable resource of salt-responsive genes for future studies to improve tomato salt tolerance.
... Since then, grape studies entered the genome era, and PN40024 became the most popular reference genome in grape studies. In the last 16 years, the PN40024 genome has been updated at least four times, with more than nine annotated versions [4,5] (Table 1). Finally, the highquality telomere-to-telomere (T2T) genome PN40024 was released in 2023 [6]. ...
Grape genome is the basis for grape studies and breeding, which is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made a substantial progress in the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, these works provide essential data for future pan-genome analysis. Apart from the de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers explored domestications and origin of grape and clarified the gene flow that occurred during the dispersed history. Moreover, GWAS and other methods were used to identify more than 900 genes related to the resistance, quality, and developmental phases of grape. These findings have benefit grape studies and provide some basis for smart genomic selection breeding. Otherwise, the grape genome has played a great role in grape studies and industries, and the importance of genomics will increase sharply in the future.
