Annotating genomes with massive-scale RNA sequencing

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.

Next-generation transcriptome assembly

“…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 .…”

“…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.…”

Genome-wide analysis of cell wall-related genes in Tuber melanosporum

“…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/).…”

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

“…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).…”