2019
DOI: 10.1186/s12864-019-6243-7
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BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

Abstract: BackgroundThe time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.ResultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts – BaRTv1.0) has been gener… Show more

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Cited by 53 publications
(66 citation statements)
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References 62 publications
(110 reference statements)
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“…RS31 showed a 2.7-fold increase in Otis and 3.6-fold in Baroness, while SCL30 showed a 1.7-fold increase in Otis and 2.5-fold increase in Baronesse in response to the drought stress ( Figure 7A ). Gene expression analysis using the barley reference transcript dataset allowed quantification of individual transcript isoforms and to determine significant DAS events using the 3D RNA-seq App (Rapazote-Flores et al, 2019 ). To identify significant DAS genes, expression changes of a log2 fold change between gene transcripts were determined along with an adjusted p < 0.01 and a minimum 0.1 (10%) change in the proportion of spliced transcripts (Δ Percent Spliced – ΔPS).…”
Section: Resultsmentioning
confidence: 99%
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“…RS31 showed a 2.7-fold increase in Otis and 3.6-fold in Baroness, while SCL30 showed a 1.7-fold increase in Otis and 2.5-fold increase in Baronesse in response to the drought stress ( Figure 7A ). Gene expression analysis using the barley reference transcript dataset allowed quantification of individual transcript isoforms and to determine significant DAS events using the 3D RNA-seq App (Rapazote-Flores et al, 2019 ). To identify significant DAS genes, expression changes of a log2 fold change between gene transcripts were determined along with an adjusted p < 0.01 and a minimum 0.1 (10%) change in the proportion of spliced transcripts (Δ Percent Spliced – ΔPS).…”
Section: Resultsmentioning
confidence: 99%
“…The RNA-seq data had 4 treatment groups: Otis, drought treatment (OD) Otis, watered treatment (OW); Baronesse drought treatment (BD) and Baronesse, watered treatment (BW) and each had 3 biological replicates (12 samples in total). Transcript quantifications were generated using Salmon (Patro et al, 2017 ) and the Barley transcriptome BARTv1.0-QUASI ( https://ics.hutton.ac.uk/barleyrtd/index.html ) (Rapazote-Flores et al, 2019 ). The 3D RNA-seq analysis App was used for differential expression (DE) and differential alternative splicing (DAS) analysis (Calixto et al, 2018 ; Guo et al, 2019 ).…”
Section: Methodsmentioning
confidence: 99%
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“…We used the Mikado pipeline (Mikado v1.2.4; Venturini et al, 2018 ) to join the different strands of transcriptome evidence, generated above. As additional transcript evidence from a more complete transcriptome we included the BaRTv1 transcripts ( Rapazote-Flores et al, 2019 ). The BaRTv1 transcripts were mapped to the Golden Promise reference assembly (GMAP version 2018-07-04; -n 0 –min-trimmed-coverage = 0.80 –min-identity = 0.90).…”
Section: Methodsmentioning
confidence: 99%
“…Up to 95% of human and 70% of plant multi-exonic genes are alternatively spliced (Pan et al, 2008;Marquez et al, 2012;Chamala et al, 2015;Zhang et al, 2017b). Further studies report that about 50% of the genes in soybeans, 46% in rice, 40% in maize, and over 60% in tomatoes and barley undergo AS (Thatcher et al, 2014;Chamala et al, 2015;Clark et al, 2019;Rapazote-Flores et al, 2019), emphasizing its importance in crop plant development and environmental response. AS has a broad role in many aspects of plant biology, but its role in responding to DNA damage is mostly unknown and requires further investigation.…”
Section: Overview Of Alternative Splicingmentioning
confidence: 99%