Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cDNA library
Changsoo Kim1, Cheol Seong Jang1, Terry L Kamps1
1Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
Functional Plant Biology : FPB
|July 22, 2020
Summary
Researchers created a normalized cDNA library from Bermudagrass to study its transcriptome. This study identified 9414 unigenes and potential DNA markers, advancing turfgrass genomics research.
Area of Science:
- Plant genomics
- Molecular biology
- Bioinformatics
Background:
- Understanding the Bermudagrass (Cynodon dactylon L.) transcriptome is crucial for turfgrass research.
- Expressed Sequence Tags (ESTs) provide valuable genetic information for plant species.
Purpose of the Study:
- To construct a normalized cDNA library from Bermudagrass to analyze its expressed sequence tags (ESTs).
- To identify unigenes and potential DNA markers for genetic studies and comparative genomics in turfgrass.
Main Methods:
- Construction of a normalized cDNA library from Bermudagrass.
- Clustering of high-quality ESTs using The Institute for Genomic Research (TIGR) Gene Indices tools to generate a unigene set.
- Comparative genomic analysis using BLAST, InterProScan, and Gene Ontology.
- Identification of EST-derived simple sequence repeats (EST-SSRs) and conserved-intron scanning primers (CISPs).
Main Results:
- A total of 15,588 high-quality ESTs were generated, resulting in 9414 unigenes.
- The normalization procedure was effective, with only 39.6% of ESTs being redundant.
- Identified candidate EST-SSRs and CISPs with potential utility as DNA markers for grasses.
Conclusions:
- The generated unigene set provides a valuable resource for Bermudagrass genomics.
- Identified EST-derived markers are expected to facilitate comparative genomic studies across grass species.
- This knowledge empowers turfgrass research by providing gene homologues for important functions.
