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Title: Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics

Abstract

Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

Authors:
 [1];  [1];  [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1023293
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Plant Science
Additional Journal Information:
Journal Volume: In press; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; ARABIDOPSIS; BIOETHANOL; BIOMASS; BIOSYNTHESIS; CELL WALL; CROPS; ETHANOL; FUNCTIONAL ANALYSIS; FUNCTIONALS; GENES; PRODUCTION

Citation Formats

Yang, Xiaohan, Ye, Chuyu, Bisaria, Anjali, Tuskan, Gerald A, and Kalluri, Udaya C. Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics. United States: N. p., 2011. Web. doi:10.1016/j.plantsci.2011.01.020.
Yang, Xiaohan, Ye, Chuyu, Bisaria, Anjali, Tuskan, Gerald A, & Kalluri, Udaya C. Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics. United States. https://doi.org/10.1016/j.plantsci.2011.01.020
Yang, Xiaohan, Ye, Chuyu, Bisaria, Anjali, Tuskan, Gerald A, and Kalluri, Udaya C. 2011. "Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics". United States. https://doi.org/10.1016/j.plantsci.2011.01.020.
@article{osti_1023293,
title = {Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics},
author = {Yang, Xiaohan and Ye, Chuyu and Bisaria, Anjali and Tuskan, Gerald A and Kalluri, Udaya C},
abstractNote = {Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.},
doi = {10.1016/j.plantsci.2011.01.020},
url = {https://www.osti.gov/biblio/1023293}, journal = {Plant Science},
number = 6,
volume = In press,
place = {United States},
year = {Sat Jan 01 00:00:00 EST 2011},
month = {Sat Jan 01 00:00:00 EST 2011}
}