Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
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DOI：
10.1111/tpj.12616
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发表时间：
2014-10-01
期刊：
影响因子：
7.2
通讯作者：
Peters, Sander
中科院分区：
文献类型：
--
作者：
Aflitos, Saulo;Schijlen, Elio;Peters, Sander
我们通过对84份番茄种质和代表番茄、奥秘、Eriopersicon和新番茄组的相关野生物种进行测序来探索遗传变异，这产生了大量关于番茄进化枝序列多样性的宝贵数据。重建了三个新的参考基因组，以支持我们的比较基因组分析。比较序列比对显示组，物种和加入特定的多态性，解释特征的果实性状和生长习性的各种品种。使用来自注释的海因茨1706参考基因组的基因模型，我们观察到与随机基因组相比，果实多样化和植物生长基因中的非同义和同义SNP（dN/dS）之间的比率的差异，表明作物种质和野生物种之间的正选择和选择压力的差异。在野生物种中，单核苷酸多态性（SNP）的数量超过1000万，即比大多数作物种质中发现的高20倍，表明作物和传家宝番茄的遗传侵蚀严重。此外，最高水平的杂合性被发现为异花授粉的自交不亲和的野生物种，而兼性和自花授粉的自交亲和的物种显示较低的杂合性水平。使用全基因组SNP信息的最大似然分析，我们实现了完整的树分辨率，而最大似然树的基础上从10个水果和生长基因的SNP显示不完全分辨率的作物加入，部分原因是杂合SNP的影响。最后，结果表明，系统发育关系与生境相关，表明这些群体内的地理小种的发生，这是茄属基因组进化研究的实际意义。
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 10million, 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.