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

Journal Article · Thu Jan 01 00:00:00 EST 2009 · Genomics

DOI:https://doi.org/10.1016/j.ygeno.2009.01.002· OSTI ID:953655

Yang, Xiaohan ^[1]; Jawdy, Sara ^[1]; Tschaplinski, Timothy J ^[1]; Tuskan, Gerald A ^[1]

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1. ORNL

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 953655
• Journal Information: Genomics, Vol. 93, Issue 5; ISSN 0888-7543
• Country of Publication: United States
• Language: English

Related Subjects

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