title: Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
abstract: We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
authors.forename: Saulo
authors.initials: S
authors.lastname: Aflitos
authors.forename: Elio
authors.initials: E
authors.lastname: Schijlen
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
authors.forename: Sandra
authors.initials: S
authors.lastname: Smit
authors.forename: Richard
authors.initials: R
authors.lastname: Finkers
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Likai
authors.initials: L
authors.lastname: Mao
authors.forename: Freek
authors.initials: F
authors.lastname: Bakker
authors.forename: Rob
authors.initials: R
authors.lastname: Dirks
authors.forename: Timo
authors.initials: T
authors.lastname: Breit
authors.forename: Barbara
authors.initials: B
authors.lastname: Gravendeel
authors.forename: Henk
authors.initials: H
authors.lastname: Huits
authors.forename: Darush
authors.initials: D
authors.lastname: Struss
authors.forename: Ruth
authors.initials: R
authors.lastname: Swanson-Wagner
authors.forename: Hans
authors.initials: H
authors.lastname: van Leeuwen
authors.forename: Roeland C H J
authors.initials: RC
authors.lastname: van Ham
authors.forename: Laia
authors.initials: L
authors.lastname: Fito
authors.forename: Laëtitia
authors.initials: L
authors.lastname: Guignier
authors.forename: Myrna
authors.initials: M
authors.lastname: Sevilla
authors.forename: Philippe
authors.initials: P
authors.lastname: Ellul
authors.forename: Eric
authors.initials: E
authors.lastname: Ganko
authors.forename: Arvind
authors.initials: A
authors.lastname: Kapur
authors.forename: Emannuel
authors.initials: E
authors.lastname: Reclus
authors.forename: Bernard
authors.initials: B
authors.lastname: de Geus
authors.forename: Henri
authors.initials: H
authors.lastname: van de Geest
authors.forename: Bas
authors.initials: B
authors.lastname: Te Lintel Hekkert
authors.forename: Jan
authors.initials: J
authors.lastname: van Haarst
authors.forename: Lars
authors.initials: L
authors.lastname: Smits
authors.forename: Andries
authors.initials: A
authors.lastname: Koops
authors.forename: Gabino
authors.initials: G
authors.lastname: Sanchez-Perez
authors.forename: Adriaan W
authors.initials: AW
authors.lastname: van Heusden
authors.forename: Richard
authors.initials: R
authors.lastname: Visser
authors.forename: Zhiwu
authors.initials: Z
authors.lastname: Quan
authors.forename: Jiumeng
authors.initials: J
authors.lastname: Min
authors.forename: Li
authors.initials: L
authors.lastname: Liao
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wang
authors.forename: Guangbiao
authors.initials: G
authors.lastname: Wang
authors.forename: Zhen
authors.initials: Z
authors.lastname: Yue
authors.forename: Xinhua
authors.initials: X
authors.lastname: Yang
authors.forename: Na
authors.initials: N
authors.lastname: Xu
authors.forename: Eric
authors.initials: E
authors.lastname: Schranz
authors.forename: Erik
authors.initials: E
authors.lastname: Smets
authors.forename: Rutger
authors.initials: R
authors.lastname: Vos
authors.forename: Johan
authors.initials: J
authors.lastname: Rauwerda
authors.forename: Remco
authors.initials: R
authors.lastname: Ursem
authors.forename: Cees
authors.initials: C
authors.lastname: Schuit
authors.forename: Mike
authors.initials: M
authors.lastname: Kerns
authors.forename: Jan
authors.initials: J
authors.lastname: van den Berg
authors.forename: Wim
authors.initials: W
authors.lastname: Vriezen
authors.forename: Antoine
authors.initials: A
authors.lastname: Janssen
authors.forename: Erwin
authors.initials: E
authors.lastname: Datema
authors.forename: Torben
authors.initials: T
authors.lastname: Jahrman
authors.forename: Frederic
authors.initials: F
authors.lastname: Moquet
authors.forename: Julien
authors.initials: J
authors.lastname: Bonnet
authors.forename: Sander
authors.initials: S
authors.lastname: Peters
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D005638:Fruit / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics*; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant
keywords: Solanum arcanum; Solanum genetic diversity; Solanum habrochaites; Solanum lycopersicum; Solanum pennellii; chromosome evolution; comparative sequence analysis; heterozygosity; introgression; phylogenomics