Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data

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• 作者：Xin Chen ; Qin Ma ; Xiaolan Rao ; Yuhong Tang ; Yan Wang ; Gaoyang Li…
• 关键词：Switchgrass ; Plant cell wall ; Homology mapping ; Co ; expression analysis
• 刊名：BioEnergy Research
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：9
• 期：1
• 页码：172-180
• 全文大小：1,017 KB
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• 作者单位：Xin Chen (1) (2) (3)
  Qin Ma (2) (3) (6)
  Xiaolan Rao (3) (4)
  Yuhong Tang (3) (5)
  Yan Wang (1)
  Gaoyang Li (1) (2)
  Chi Zhang (2)
  Xizeng Mao (2) (7)
  Richard A. Dixon (3) (4)
  Ying Xu (1) (2) (3) (8)
  
  1. College of Computer Science and Technology, and School of Public Health, Jilin University, Changchun, China
  2. Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
  3. US Department of Energy, BioEnergy Science Center (BESC), Oak Ridge, TN, 37831, USA
  6. Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA
  4. Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
  5. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
  7. Institute of Applied Cancer Center, MD Anderson Cancer Center, Houston, TX, 77054, USA
  8. A110 Life Science building, University of Georgia, Athens, GA, 30602, USA
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Biomaterials
  Biochemical Engineering
  Bioorganic Chemistry
  
• 出版者：Springer New York
• ISSN：1939-1242

文摘

Large numbers of plant cell-wall (CW)-related genes have been identified or predicted in several plant genomes such as Arabidopsis thaliana, Oryza sativa (rice), and Zea mays (maize), as results of intensive studies of these organisms in the past 2 decades. However, no such gene list has been identified in switchgrass (Panicum virgatum), a key bioenergy crop. Here, we present a computational study for prediction of CW genes in switchgrass using a two-step procedure: (i) homology mapping of all annotated CW genes in the fore-mentioned species to switchgrass, giving rise to a total of 991 genes, and (ii) candidate prediction of CW genes based on switchgrass genes co-expressed with the 991 genes under a large number of experimental conditions. Specifically, our co-expression analyses using the 991 genes as seeds led to the identification of 104 large clusters of co-expressed genes, each referred to as a co-expression module (CEM), covering 830 of the 991 genes plus 823 additional genes that are strongly co-expressed with some of the 104 CEMs. These 1653 genes represent our prediction of CW genes in switchgrass, 112 of which are homologous to predicted CW genes in Arabidopsis. Functional inference of these genes is conducted to derive the possible functional relations among these predicted CW genes. Overall, these data may offer a highly useful information source for cell-wall biologists of switchgrass as well as plants in general.