Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq

BMC Plant Biology

Research Article

Maria R Ercolano¹  Graham J Etherington²  Kamil Witek²  Jonathan D G Jones²  Florian Jupe²  Giuseppe Andolfo³ 

[1] Department of Agriculture Sciences, University of Naples ‘Federico II’, Via Universita’ 100, 80055, Portici, Italy;The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, UK;The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, UK;Department of Agriculture Sciences, University of Naples ‘Federico II’, Via Universita’ 100, 80055, Portici, Italy;

关键词: RenSeq;    NB-LRR;    cDNA;    Gene model;    Disease resistance;    Paralogous;    Plant breeding;    Solanum lycopersicum;    Solanum pimpinellifolium;    Arabidopsis thaliana;   

DOI  :  10.1186/1471-2229-14-120

 received in 2013-12-19, accepted in 2014-04-17,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recently, we developed the RenSeq method to reannotate the full NB-LRR gene complement in potato and to identify novel sequences that were not picked up by the automated gene prediction software. Here, we established RenSeq on the reference genome of tomato (Solanum lycopersicum) Heinz 1706, using 260 previously identified NB-LRR genes in an updated Solanaceae RenSeq bait library.ResultUsing 250-bp MiSeq reads after RenSeq on genomic DNA of Heinz 1706, we identified 105 novel NB-LRR sequences. Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. pimpinellifolium LA1589 genome, RenSeq enabled the annotation of 355 NB-LRR genes. The majority of these are however fragmented, with 5′- and 3′-end located on the edges of separate contigs. Phylogenetic analyses show a high conservation of all NB-LRR classes between Heinz 1706, LA1589 and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor. A phylogenetic comparison to the Arabidopsis thaliana NB-LRR complement verifies the high conservation of the more ancient CCRPW8-type NB-LRRs. Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues.ConclusionRenSeq is a promising method to facilitate analysis of plant resistance gene complements. The reannotated tomato NB-LRR complements, phylogenetic relationships and chromosomal locations provided in this paper will provide breeders and scientists with a useful tool to identify novel disease resistance traits. cDNA RenSeq enables for the first time next-gen sequencing approaches targeted to this very low-expressed gene family without the need for normalization.

【 授权许可】

Unknown   
© Andolfo et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.