Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Creators: name: Aflitos, Saulo A.
name: Schijlen, Elio
name: Finkers, Richard
name: Smit, Sandra
name: Wang, Jun
name: Zhang, Gengyun
name: Li, Ning
name: Mao, Likai
name: de Jong, Hans
name: Bakker, Freek
name: Gravendeel, Barbara
name: Breit, Timo
name: Dirks, Rob
name: Huits, Henk
name: Struss, Darush
name: Wagner, Ruth
name: van Leeuwen, Hans
name: van Ham, Roeland
name: Fito, Laia
name: Guigner, Laëtitia
name: Sevilla, Myrna
name: Ellul, Philippe
name: Ganko, Eric W.
name: Kapur, Arvind
name: Reclus, Emmanuel
name: de Geus, Bernard
name: van de Geest, Henri
name: Hekkert, Bas te Lintel
name: Van Haarst, Jan C.
name: Smits, Lars
name: Koops, Andries
name: Perez, Gabino Sanchez
name: de Ridder, Dick
name: van Heusden, Sjaak
name: Visser, Richard
name: Quan, Zhiwu
name: Min, Jiumeng
name: Liao, Li
name: Wang, Xiaoli
name: Wang, Guangbiao
name: Yue, Zhen
name: Yang, Xinhua
name: Xu, Na
name: Schranz, Eric
name: Smets, Eric F.
name: Vos, Rutger A.
name: Rauwerda, Han
name: Ursem, Remco
name: Schuit, Cees
name: Kerns, Mike
name: Berg, Jan van den
name: Vriezen, Wim H.
name: Janssen, Antoine
name: Jahrman, Torben
name: Moquet, Frederic
name: Bonnet, Julien
name: Peters, Sander A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a reconstruction of three new reference genomes in support of our comparative genome analyses. Sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. This is reflected by the SNP count in wild species which can exceed 10 million i.e. 20 fold higher than in crop accessions. Comparative sequence alignment reveals group, species, and accession specific polymorphisms, which explain characteristic fruit traits and growth habits in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, which probably is the result of a positive selection. We detected highly divergent segments in wild S. lycopersicum species, and footprints of introgressions in crop accessions originating from a common donor accession. Phylogenetic relationships of fruit diversification and growth specific genes from crop accessions show incomplete resolution and are dependent on the introgression donor. In contrast, whole genome SNP information has sufficient power to resolve the phylogenetic placement of each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding. Our study illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies.
description: 4 Figure, 10 Supplementary Figures, 2 Supplementary Figures This is the pre-peer reviewed version of the following article: The Plant Journal 80.1 (2014): 136-148, which has been published in final form at http://doi.org/10.1111/tpj.12616