Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass.
Switchgrass is a large, North American, perennial grass that is being evaluated as a potential energy crop. Expressed sequence tags (ESTs) were generated from four switchgrass cv. "Kanlow" cDNA libraries to create a gene inventory of 7,810 unique gene clusters from a total of 11,990 individual sequences. Blast similarity searches to SwissProt and GenBank non-redundant protein and nucleotide databases were performed and a total of 79% of these unique clusters were found to be similar to existing protein or nucleotide sequences. Tentative functional classification of 61% of the sequences was possible by association with appropriate gene ontology descriptors. Significant differential representation between genes in leaf, stem, crown, and callus libraries was observed for many highly expressed genes The unique gene clusters were screened for the presence of short tandem repeats for further development as microsatellite markers. A total of 334 gene clusters contained repeats representing 3.8% of the ESTs queried.
Tobias
Christian M
CM
USDA, ARS, Western Regional Research Center, Genomics and Gene Discovery Unit, Albany, CA 94710, USA. ctobias@pw.usda.gov
Twigg
Paul
P
Hayden
Daniel M
DM
Vogel
Kenneth P
KP
Mitchell
Rob M
RM
Lazo
Gerard R
GR
Chow
Elaine K
EK
Sarath
Gautam
G
D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant; D008897:Panicum / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D018547:Plant Stems / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*
D018744:DNA, Plant; D010940:Plant Proteins