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Protocols in ecological and environmental plant physiology


Article << Previous     |     Next >>   Contents Vol 35(7)

Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cDNA library

Changsoo Kim A, Cheol Seong Jang A B, Terry L. Kamps A C, Jon S. Robertson A, Frank A. Feltus A D, Andrew H. Paterson A E

A Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
B Present address: Institute of Life Science and Natural Resources, Korea University, Seoul, Korea.
C Present address: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.
D Present address: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
E Corresponding author. Email: paterson@uga.edu
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A normalised cDNA library was constructed from Bermudagrass to gain insight into the transcriptome of Cynodon dactylon L. A total of 15 588 high-quality expressed sequence tags (ESTs) from the cDNA library were subjected to The Institute for Genomic Research Gene Indices clustering tools to produce a unigene set. A total of 9414 unigenes were obtained from the high-quality ESTs and only 39.6% of the high-quality ESTs were redundant, indicating that the normalisation procedure was effective. A large-scale comparative genomic analysis of the unigenes was carried out using publicly available tools, such as BLAST, InterProScan and Gene Ontology. The unigenes were also subjected to a search for EST-derived simple sequence repeats (EST-SSRs) and conserved-intron scanning primers (CISPs), which are useful as DNA markers. Although the candidate EST-SSRs and CISPs found in the present study need to be empirically tested, they are expected to be useful as DNA markers for many purposes, including comparative genomic studies of grass species, by virtue of their significant similarities to EST sequences from other grasses. Thus, knowledge of Cynodon ESTs will empower turfgrass research by providing homologues for genes that are thought to confer important functions in other plants.

Keywords: conserved-intron scanning primer, expressed sequence tag, golf courses, simple sequence repeat.

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