Enhancing faba bean (Vicia faba L.) genome resources

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13Gb) genome. In order to address this challenge, RNA-seq analysis was performed on faba bean (cv Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16,300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10 % could be aligned to known repetitive genetic elements. Over 26,000 of the reference transcriptome unigenes could be aligned to DNA-seq reads with high confidence. Moreover, this comparison identified 56,668 potential splice points in all identified unigenes. Sequence length data was extended at 461 putative loci through alignment of DNA-seq contigs to full length, publically available linkage marker sequences. Reads also yielded coverages of 3466x and 650x for the chloroplast and mitochondrial genomes respectively. Inter- and intra-species organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes.