Enhancing faba bean (Vicia faba L.) genome resources

Publication Overview
TitleEnhancing faba bean (Vicia faba L.) genome resources
AuthorsCooper JW, Wilson MH, Derks MFL, Smit S, Kunert KJ, Cullis C, Foyer CH
TypeJournal Article
Journal NameJournal of experimental botany
Year2017
CitationCooper JW, Wilson MH, Derks MFL, Smit S, Kunert KJ, Cullis C, Foyer CH. Enhancing faba bean (Vicia faba L.) genome resources. Journal of experimental botany. 2017 Apr 17.

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.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1460-2431
eISSN1460-2431
Publication Date2017 Apr 17
Journal AbbreviationJ. Exp. Bot.
DOI10.1093/jxb/erx117
Elocation10.1093/jxb/erx117
Copyright© The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland