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Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans.

Author(s): Bastos RW, Valero C, Silva LP, Schoen T, Drott M, Brauer V, Silva-Rocha R, Lind A, Steenwyk JL, Rokas A, Rodrigues F, Resendiz-Sharpe A, Lag...

mSphere. 2020 Apr 08;5(2): Authors: Bastos RW, Valero C, Silva LP, Schoen T, Drott M, Brauer V, Silva-Rocha R, Lind A, Steenwyk JL, Rokas A, Rodrigues F, Resendiz-Sharpe A, Lagrou K, Marcet-Houben...

Article GUID: 32269156
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

Author(s): Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A

BMC Bioinformatics. 2014 Jul 01;15:229 Authors: Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A

Article GUID: 24980894
Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.

Author(s): Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Methods Mol Biol. 2017;1588:279-298 Authors: Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Article GUID: 28417376
Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.

Author(s): Reid I

Methods Mol Biol. 2018;1775:209-227 Authors: Reid I

Article GUID: 29876820
Title:Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.
Authors:Gruninger RJ,  Reid I,  Forster RJ,  Tsang A,  McAllister TA
Link:https://www.ncbi.nlm.nih.gov/pubmed/28417376?dopt=Abstract
DOI:10.1007/978-1-4939-6899-2_21
Category:Methods Mol Biol
PMID:28417376
Dept Affiliation: GENOMICS
1 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, AB, Canada, T1J 4B1. robert.gruninger@agr.gc.ca.
2 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
3 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, AB, Canada, T1J 4B1.

Description:

Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.

Methods Mol Biol. 2017;1588:279-298

Authors: Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Abstract

Lignocellulosic biomass represents an abundant, renewable resource that can be used to produce biofuels, low-cost livestock feed, and high-value chemicals. The potential of this resource has led to intensive research efforts to develop cost effective methods to breakdown lignocellulose. The efficiency with which the anaerobic fungi (phylum Neocallimastigomycota) degrade plant biomass is well recognized and in recent years has received renewed interest. Transcriptomics has been used to identify enzymes that are expressed by these fungi and are involved in the degradation of a range of lignocellulose feedstocks. The transcriptome is the entire complement of coding and noncoding RNA transcripts that are expressed by a cell under a particular set of conditions. Monitoring changes in gene expression can provide fundamental information about the biology of an organism. Here we outline a general methodology that will enable researchers to conduct comparative transcriptomic studies with the goal of identifying enzymes involved in the degradation of the plant cell wall. The method described here includes growth of fungal cultures, isolation and sequencing of RNA, and a basic description of data analysis for bioinformatic identification of differentially expressed transcripts.

PMID: 28417376 [PubMed - indexed for MEDLINE]