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ARS Home » Midwest Area » Lexington, Kentucky » Forage-animal Production Research » Research » Publications at this Location » Publication #318672

Research Project: Sustainable Forage-Based Production for the Mid-South Transition Zone

Location: Forage-animal Production Research

Title: De novo transcriptome assembly and dynamic spatial gene expression analysis in red clover (Trifolium pratense)

Author
item Chakrabarti, Manohar
item Dinkins, Randy
item Hunt, Arthur

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/9/2015
Publication Date: 12/15/2015
Citation: Chakrabarti, M., Dinkins, R.D., Hunt, A.G. 2015. De novo transcriptome assembly and dynamic spatial gene expression analysis in red clover (Trifolium pratense). The Plant Genome. doi: 10.3835/plantgenome2015.06.0048.

Interpretive Summary: Red clover is a cool-season forage legume that provides high value feed to livestock grown throughout the Northeastern USA. Red clover is the most widely planted forage legume after alfalfa. A de novo transcriptome assembly of red clover (variety ‘Kenland’) was constructed from leaf, root and flowers tissues. The draft assembly consists of 37,565 genes. A high degree of gene conservation between red clover and other legumes, namely, barrel medic, soybean, and common bean was found. The assembled transcriptome was annotated to allow identification of individual genes. A comparative gene expression analysis between different tissue types was performed using the assembled transcriptome as the reference, revealing dynamic gene expression patterns across different tissues and also allowed for identification of genes expressed in specific tissues. Genes expressed in a tissue specific manner will aid in future research focusing on developmental studies or for future genetic improvement of red clover.

Technical Abstract: Red clover (Trifolium pratense L.) is a cool season forage legume, grown throughout the Northeastern USA and is the most widely planted forage legume after alfalfa. Red clover provides high value feed to the livestock because of high protein content and easy digestibility. To date, genomic resources for red clover are scarce. In the current study a de novo transcriptome assembly of red clover was constructed, representing different tissue types. The draft assembly consists of 37,565 contigs with N50 and average contig length of 1,707 and 1,262 bp, respectively. A comparative study with three other legume species displayed high degree of sequence conservation between red clover and other legumes. The assembled transcriptome was annotated to allow identification of desirable genes. In particular, a genome-wide identification of red clover transcripts encoding putative transcription factors was carried out. A comparative gene expression analysis between different tissue types was performed using the assembled transcriptome as the reference, which revealed dynamic gene expression patterns across different tissue types and also identified tissue specific gene co-expression clusters. Genes representing tissue specific clusters were subjected to Gene Ontology enrichment analysis to identify over- represented functional groups. Identification of these tissue-specific gene expression clusters can help in future research focusing on developmental studies across tissues or in biotechnological improvement of red clover.