Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 68, Issue 8, Pages 1941-1953Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/erx117
Keywords
Illumina sequencing; legumes; mitochondrial genome; plastome; protein security; RNA-seq analysis
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Funding
- BBSRC CASE studentship [BB/K501839/1]
- Wherry and Sons Ltd
- Old School, High Street, Rippingale, Lincolnshire, UK
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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 (similar to 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 similar to 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 3466x and 650x 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.
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