Abstract:Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.
“…Full-length variants can be assembled from only a few folds of sequencing depth 22 , and small gaps in read coverage can be filled using the reference sequence 18 . Similarly, this strategy tends to generate longer UTRs, since it recovers the ends of the transcripts, which usually have lower sequencing coverage 17 .…”
Section: Reference-based Strategymentioning
confidence: 99%
“…In this review, we summarize these exciting breakthroughs that have resulted in a wealth of assembled transcriptomes from short reads [16][17][18][19][20][21][22][23][24][25][26][27] , while providing practical guidelines for implementing a transcriptome assembly experiment. We discuss the experimental and informatics considerations that need to be made before assembly, such as RNA-Seq library construction, data pre-processing and how to assess the assembly quality.…”
“…Full-length variants can be assembled from only a few folds of sequencing depth 22 , and small gaps in read coverage can be filled using the reference sequence 18 . Similarly, this strategy tends to generate longer UTRs, since it recovers the ends of the transcripts, which usually have lower sequencing coverage 17 .…”
Section: Reference-based Strategymentioning
confidence: 99%
“…In this review, we summarize these exciting breakthroughs that have resulted in a wealth of assembled transcriptomes from short reads [16][17][18][19][20][21][22][23][24][25][26][27] , while providing practical guidelines for implementing a transcriptome assembly experiment. We discuss the experimental and informatics considerations that need to be made before assembly, such as RNA-Seq library construction, data pre-processing and how to assess the assembly quality.…”
“…Expression levels of the annotated genes were also detected by massive cDNA sequencing of the abovementioned FLM, ECM and FB libraries with the Solexa/Illumina technology. Deep sequencing was carried out at the Genoscope facilities as described in Denoeud et al (2008) and mapped to the T. melanosporum genome and gene models, as reported by Martin et al (2010). The single-end reads obtained were 36 nucleotides long and were deposited in the Tuber Gbrowse (http://mycor.nancy.inra.fr/cgi-bin/secure/gbrowse/).…”
“…Under HS, enrichment of binding sites for HSFs, bZIPs and DREBs were observed, along with the increase in the expression of different families of TFs (Sarkar et al, 2014). Similarly, we used ab initio method for the functional annotation of transcripts using the dataset of Arabidopsis and Z. mays; now-days, ab initio method is frequently used to assemble a transcriptome for interpreting the annotated transcripts (Denoeud et al, 2008;Guttman et al, 2010;Trapnell et al, 2010).…”
Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22°-3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.
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