Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Saulo A. Aflitos, Elio Schijlen, Richard Finkers, Sandra Smit, Jun Wang, Gengyun Zhang, Ning Li, Likai Mao, Hans de Jong, Freek Bakker, Barbara Gravendeel, Timo Breit, Rob Dirks, Henk Huits, Darush Struss, Ruth Wagner, Hans van Leeuwen, Roeland van Ham, Laia Fito, Laëtitia Guigner, Myrna Sevilla, Philippe Ellul, Eric W. Ganko, Arvind Kapur, Emmanuel Reclus, Bernard de Geus, Henri van de Geest, Bas te Lintel Hekkert, Jan C. Van Haarst, Lars Smits, Andries Koops, Gabino Sanchez Perez, Dick de Ridder, Sjaak van Heusden, Richard Visser, Zhiwu Quan, Jiumeng Min, Li Liao, Xiaoli Wang, Guangbiao Wang, Zhen Yue, Xinhua Yang, Na Xu, Eric Schranz, Eric F. Smets, Rutger A. Vos, Han Rauwerda, Remco Ursem, Cees Schuit, Mike Kerns, Jan van den Berg, Wim H. Vriezen, Antoine Janssen, Torben Jahrman, Frederic Moquet, Julien Bonnet, Sander A. Peters
(Submitted on 21 Apr 2015)

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.

Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Robert Kofler , Christian Schlötterer
doi: http://dx.doi.org/10.1101/018218

Transposable elements (TEs) are major drivers of genomic and phenotypic evolution, yet many questions about their biology remain poorly understood. Here, we compare TE abundance between populations of the two sister species D. mauritiana und D. simulans and relate it to the more distantly related D. melanogaster. The low population frequency of most TE insertions in D. melanogaster and D. simulans has been a key feature of several models of TE evolution. In D. mauritiana, however, the majority of TE insertions are fixed (66%). We attribute this to a lower transposition activity of up to 47 TE families in D. mauritiana, rather than stronger purifying selection. Only three families, including the extensively studied Mariner, may have a higher activity in D. mauritiana. This remarkable difference in TE activity between two recently diverged Drosophila species (≈ 250,000 years), also supports the hypothesis that TE copy numbers in Drosophila may not reflect a stable equilibrium where the rate of TE gains equals the rate of TE losses by negative selection. We propose that the transposition rate heterogeneity results from the contrasting ecology of the two species: the extent of vertical extinction of TE families and horizontal acquisition of active TE copies may be very different between the colonizing D. simulans and the island endemic D. mauritiana. Our findings provide novel insights in the evolution of TEs in Drosophila and suggest that the ecology of the host species could be a major, yet underappreciated, factor governing the evolutionary dynamics of TEs.