The genome of the stress-tolerant wild tomato species Solanum pennellii

Abstract

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum 1 . Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance 2 . Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.Crosses between distantly related plants can lead to substantial improvements in performance. Notably, S. pennellii × S. lycopersicum ILs have been used to define numerous quantitative trait loci (QTLs) for superior yield, chemical composition, morphology, abiotic stress tolerance and extreme heterosis 3,4 . Although genetic studies have proven informative, few genes underlying specific QTLs have been cloned, largely because of the lack of a S. pennellii genome sequence. To support QTL analyses, we sequenced the genome of S. pennellii using Illumina sequencing with ~190-fold coverage ( Fig. 1 and Supplementary Tables 1-5). The initial assembly size was 942 Mb, with a scaffold N50 value of 1.7 Mb and N90 value of 0.43 Mb (Table 1 and Supplementary Tables 6 and 7). We estimated the total genome size to be about 1.2 Gb using a k-mer-based analysis ( Supplementary Fig. 1 and Supplementary Table 8), in accordance with previous estimations 3,4 . We anchored 97.1% of the genome assembly to chromosomes using genetic maps and restriction site-associated DNA sequencing (RAD-seq)-based markers from the IL population 5 (Supplementary Note). Comparison of the assembly to publicly available BAC sequences indicated an accuracy of >99.9%, and a satisfactory accuracy of gap-filled regions was shown by realigning reads (Supplementary Fig. 2 and Supplementary Table 9). Of the 307,350 S. lycopersicum and 7,812 S. pennellii publicly available ESTs, 93% and >96% could be aligned to the genome, respectively (Supplementary Table 10), indicating comprehensive coverage of the gene-rich regions. We predicted 32,273 high-confidence genes and a potential set of 44,966 protein-coding genes and checked these

Unilateral incompatibility gene ui1.1 encodes an S-locus F-box protein expressed in pollen of Solanum species

“…The tomato whole genome sequence (26) and the S. pennellii genome sequence (27) were searched for SLF coding genes. Candidate genes were annotated using GENSCAN (genes.…”

“…We identified 19 SLF genes (SlSLF-1 to -19) in the S. lycopersicum genome that mapped to the S-locus region on chromosome 1 (SI Appendix). We also searched the S. pennellii accession LA0716 genome sequence (27) using the same Petunia SLF protein to find related proteins. Four additional SLF paralogs (SpSLF-20 to -23) were identified in the S. pennellii genome that were absent from tomato (SI Appendix).…”

A feedback insensitive isopropylmalate synthase affects acylsugar composition in cultivated and wild tomato

“…Resequencing confirmed that the S. lycopersicum M82 SlIPMS3 also contains this truncation, indicating that this is a bona fide change rather than a sequence assembly error. Because introgression of the S. pennellii LA0716 region containing this gene has a major impact on acyl chain composition, we attempted to identify the orthologous gene from this accession using available sequence data (Bombarely et al, 2012;Tomato Genome Consortium, 2012;Bolger et al, 2014a). The SlIPMS3 (Solyc08g014230) and S. pennellii (Sopen08g005140) genes are reciprocal best hits, with 97% identity within a large syntenic region comprising 361 collinear genes (see "Materials and Methods").…”

“…For reciprocal best match, we performed an all-versus-all BLAST between all annotated S. lycopersicum and S. pennellii proteins (Bolger et al, 2014a) and selected pairs that were reciprocal best hits of each other at E , 1e-10. We determined genome-wide synteny between reciprocal best hits using MCScanX (Wang et al, 2013) using the default parameters.…”

Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

“…In this respect, the scientific genomic achievements in tomato have allowed fishing in its gene pool and taking advantage of the extraordinary genetic wealth of its wild relatives (Víquez-Zamora et al, 2013;Aflitos et al, 2014). In this way, tomato breeders have been able to find genetic solutions to some biotic and abiotic threats and achieving improvements to cope with unfavorable agricultural environments in a climate change scenario (Bolger et al, 2014;Thapa et al, 2015). On the contrary, up to now in common eggplant, as well as in scarlet and gboma eggplant, the use of wild relatives for the breeding purpose have been negligible and often purely academic .…”