Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome.

PloS One
Peter E LarsenFrank R Collart

Abstract

Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure. We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derived from the fungus Laccaria bicolor, which develops a mycorrhizal symbiotic association with the roots of many tree species. Our analysis focused on the subset of 1501 gene models that are differentially expressed in the free living vs. mycorrhizal transcriptome and are expected to be important elements related to carbon metabolism, membrane permeability and transport, and intracellular signaling. Of the set of 1501 gene models, 1439 (96%) successfully generated modified gene models in which all error flags were successfully resolved and the sequences ...Continue Reading

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Citations

Sep 13, 2014·Briefings in Functional Genomics·Martha Lucía MeijueiroAntonio G Pisabarro
May 17, 2011·BMC Systems Biology·Peter E LarsenFrank R Collart
Feb 3, 2016·Frontiers in Plant Science·Peter E LarsenFrank R Collart
Aug 20, 2015·Environmental Microbiology·Lucia ŽifčákováPetr Baldrian
May 3, 2011·Current Opinion in Plant Biology·Claire Veneault-Fourrey, Francis Martin
Nov 20, 2014·Frontiers in Microbiology·Alan KuoIgor V Grigoriev
Mar 7, 2017·Analytical Chemistry·Tiffany VictorLeland James Cseke

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Methods Mentioned

BETA
RNA-seq
RNAseq
PCR

Software Mentioned

fasta
âBowtie
BestModel
Bridge
BestModelv1
gff
Myc
Affymetix
Bowtie
GeneModel

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