Cooper, JW, Wilson, MH orcid.org/0000-0002-6323-6059, Derks, MFL et al. (4 more authors) (2017) Enhancing faba bean (Vicia faba L.) genome resources. Journal of Experimental Botany, 68 (8). pp. 1941-1953. ISSN 0022-0957
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 (~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.
Metadata
Item Type: | Article |
---|---|
Authors/Creators: |
|
Copyright, Publisher and Additional Information: | © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | Illumina sequencing, legumes, mitochondrial genome, plastome, protein security, RNA-seq analysis. |
Dates: |
|
Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 21 Mar 2017 11:52 |
Last Modified: | 11 Jan 2023 12:33 |
Status: | Published |
Publisher: | Oxford University Press |
Identification Number: | 10.1093/jxb/erx117 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:113925 |