De novo Transcriptome Assembly and Dynamic Spatial Gene Expression Analysis in Red Clover

Red clover (Trifolium pratense L.) is a cool-season forage legume grown throughout the northeastern United States and is the most widely planted forage legume after alfalfa (Medicago sativa L.). 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 1707 and 1262 bp, respectively. A comparative study with three other legume species displayed a 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 performed. 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 spatially dynamic gene coexpression clusters. Genes representing tissue-enriched clusters were subjected to gene ontology (GO) enrichment analysis to identify over-represented functional groups. Identification of these tissue-enriched gene coexpression clusters can help in future research focusing on developmental studies across tissues or in biotechnological improvement of red clover.