First Evaluation of the Assembly and Annotation of the Red Clover (Trifolium pratense) Genome

Red clover (Trifolium pratense L.) is a major forage legume cultivated in temperate regions. Red clover is an outcrossing species with a diploid genome (2n = 2x = 14) of approximately 430 Mbp. We assembled a total of 582 Mbp from Illumina paired end and mate pair libraries sequenced from a diploid line selected at IBERS, UK. Repetitive and low complexity regions comprised 51.7 % of the total assembly. 84.3 % of the genome (362.4 Mbp) was contained in 20,295 scaffolds longer than 8 Kbp (N50 = 19,731 bp). A gene annotation of these scaffolds resulted in 57,593 genes and 59,548 isoforms, and a total of 44,820 unique transcripts after clustering. This annotation is based on genes predicted by Augustus and GeneMark modelers, as well as alignments of Fabaceae proteins, transcripts from three related model species, and de novo and genome-guided transcripts assembled from RNAseq reads. Integration with Sanger-based bacterial artificial chromosome (BAC) end sequences and a genetic map is in progress to improve the contiguity of the assembly. The future publication of the first draft of the red clover genome will facilitate breeding improved varieties for animal feed.