康奈尔大学的James J. Giovannoni和Zhangjun Fei研究团队合作完成了番茄的泛基因组测序，并发现大量新基因以及一个参与控制番茄口味的基因。相关论文于2019年6月发表在国际学术期刊《Nature Genetics》杂志上。

现代的番茄种类含有的遗传多样性很狭窄，因此限制了遗传改良的空间。在最近这项工作中，研究人员根据在系统发育和地理分布上具有代表性的725个番茄种类的基因组序列构建了番茄泛基因图谱，从而揭示了4873个番茄参考基因组中缺失的基因。存在/缺失变异分析揭示在番茄的驯化和改良过程中，大量基因丢失，并且许多基因和启动子均存在强烈的负筛选。这些丢失或负筛选的基因主要集中在一些重要的性状，特别是疾病抗性方面。

此外，研究人员还鉴定到番茄驯化过程中TomLoxC基因启动子下一个罕见的等位基因。进一步实验表明，TomLoxC参与脱辅基类胡萝卜素（apocarotenoid）的合成，从而影响番茄的口味。在处于橙色阶段的番茄中，带有常见和罕见TomLoxC两种等位基因的杂合子番茄比只带有其中一种等位基因的纯合子番茄有着更高的TomLoxC的表达。番茄泛基因组图谱的绘制有利于完善番茄的参考基因组图谱并为未来的番茄育种提供帮助。

附：英文原文

Title: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Author: Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Jose Blanca, Joaquin Canizares, Yimin Xu, Esther van der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni, Zhangjun Fei

Issue&Volume: Volume 51 Issue 6, June 2019

Abstract: Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.

DOI: 10.1038/s41588-019-0410-2

Source:https://www.nature.com/articles/s41588-019-0410-2