Abstract:
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 (~13 Gb) genome. In order
to address this challenge, RNA-sequencing 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-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56
668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through
alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages
of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle
genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean
organelle genomes.
Description:
Table S1. List of putative splice points identified by aligning
DNA-seq reads to the CSFL.
Table S2. List of full length markers upon which the publication
of Webb et al. (2016) was based, with aligned DNA
contigs and sequence extension data.
Table S3. Pairwise alignments of sequences of identified
genes in the chloroplast and mitochondrial genomes.
