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Title: Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

Abstract

Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.

Authors:
 [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:
953655
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Genomics; Journal Volume: 93; Journal Issue: 5
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ARABIDOPSIS; BIOFUELS; CARBON SEQUESTRATION; FLOWERS; FUNCTIONALS; GENES; GLYCINE; INTRONS; MERISTEMS; PLANTS; PROTEINS; RICE; ROOTS; SORGHUM; Lineage-specific genes; Gene expression; Arabidopsis; Rice; Poplar; Perennial plants

Citation Formats

Yang, Xiaohan, Jawdy, Sara, Tschaplinski, Timothy J, and Tuskan, Gerald A. Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. United States: N. p., 2009. Web. doi:10.1016/j.ygeno.2009.01.002.
Yang, Xiaohan, Jawdy, Sara, Tschaplinski, Timothy J, & Tuskan, Gerald A. Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. United States. doi:10.1016/j.ygeno.2009.01.002.
Yang, Xiaohan, Jawdy, Sara, Tschaplinski, Timothy J, and Tuskan, Gerald A. Thu . "Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus". United States. doi:10.1016/j.ygeno.2009.01.002.
@article{osti_953655,
title = {Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus},
author = {Yang, Xiaohan and Jawdy, Sara and Tschaplinski, Timothy J and Tuskan, Gerald A},
abstractNote = {Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.},
doi = {10.1016/j.ygeno.2009.01.002},
journal = {Genomics},
number = 5,
volume = 93,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}