Solanum pennellii LA716 - Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Solanum pennellii LA716 - 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 group. In addition, we present a reconstruction of three new reference genomes in support of our comparative genome analyses. This comparative analysis elucidates species specific chromosome structural differences. Furthermore, sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. For wild species the SNP frequency increases 20 folds to more than 10 million SNPs. Our study unequivocally illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies. Comparative sequence alignment reveals group, species, and accession specific polymorphisms within domestication syndrome genes, which are explanatory for characteristic fruit traits and growth habit in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in domestication syndrome genes compared to a random set of genes which probably is the result of a positive selection. Based on whole genome SNP information, we unambiguously resolved the phylogenetic placement for 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.

潘那利番茄（Solanum pennellii）LA716：本研究以番茄支系内代表Lycopersicon组、Arcanum组、Eriopersicon组及Neolycopersicon组的84份番茄种质及相关野生近缘种为材料开展测序，以此解析番茄支系的遗传变异。此外，本研究构建了三套全新的参考基因组，为比较基因组分析提供支撑。本次比较分析阐明了物种特异性的染色体结构差异。此外，商业育种品系的序列多样性极低，提示栽培番茄已发生显著的遗传侵蚀。而野生近缘种的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）频率提升20倍，超过1000万个SNP位点。本研究明确证实，开展番茄比较基因组学及茄属（Solanum）基因组进化研究，亟需构建多套参考基因组。比较序列比对结果显示，驯化综合征基因中存在类群、物种及种质特异性的多态性，这可解释番茄种质的典型果实性状与生长习性差异。基于注释完成的亨氏（Heinz）参考基因组的基因模型，本研究发现，驯化综合征基因的dN/dS比值相较于随机选取的基因集存在偏倚，这大概率是正向选择作用的结果。基于全基因组SNP信息，本研究通过最大似然法（Maximum Likelihood）分析，明确解析了番茄支系四个主要类群中每份种质的系统发育位置。系统发育关系与物种的生境及交配类型显著相关，提示这些类群内存在地理宗，这对渐渗杂交育种工作具有重要的实践价值。