New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits

背景回顾：Peach (Prunus persica L. Batsch) is an economically important fruit crop worldwide. 

提出问题：Although a high-quality peach genome has previously been published, Sanger sequencing was used for its assembly, which generated short contigs.

主要研究：Here, we report a chromosome-level genome assembly and sequence analysis of Chinese Cling, an important founder cultivar for peach breeding programs worldwide. 

结果1-基因组组装：The assembled genome contained 247.33 megabases (Mb) with a contig N50 of 4.13 Mb and a scaffold N50 of 29.68 Mb, representing 99.8% of the estimated genome.

结果2-比较基因组：Comparisons between this genome and the recently published one (Lovell peach) uncovered a total of 685 407 single nucleotide polymorphisms, 162 655 insertions and deletions, and 16 248 structural variants.

结果3-基因家族收缩与扩张：Gene family analysis highlighted the contraction of the gene families involved in flavone, flavonol, flavonoid, and monoterpenoid biosynthesis.

结果4-香气的GWAS分析：Then, the volatile compounds of 256 peach varieties were quantitated in mature fruits in 2015 and 2016 to perform a genome wide association analysis. A comparison with the identified domestication genomic regions allowed us to find a total of 25 quantitative trait loci, associated with seven volatile compounds, in the domestication region, which is consistent with the differences in volatile compounds between wild and cultivated peaches. 

结果5-关键基因鉴定：Finally, a gene encoding terpene synthase, located within a previously reported QTL region, was identified to be associated with linalool synthesis. 

结论：Such findings highlight the importance of this new assembly for the analysis of evolutionary mechanisms and gene identification in peach species. Furthermore, this high-quality peach genome provides valuable information for future fruit improvement.

 摘 要 

桃树是全球范围上具有重要经济价值的水果作物。尽管先前已有一个高质量的桃树基因组被报道，但是其采用的还是第一代Sanger测序技术，因此拼出的contig相对比较短。本文中，作者报道了粘桃的染色体级别基因组组装，该品种的桃树被广泛用于栽培桃的育种项目。粘桃的基因组组装大小为247.33Mb，contig N50长4.13 Mb，scaffold N50长29.68 Mb，占预估基因组大小的99.8%。通过与最近发表的Lovell桃基因组比较分析，作者一共鉴定了685 407个单核苷酸多态性，162 655个插入和缺失，以及16 248个机构变异。基因家族分析显示参与黄酮、黄酮醇、类黄酮和单萜生物合成相关的基因家族发生了收缩。作者于2015年和2016年，对256份桃品种成熟果实的挥发性化合物进行了定量测定，并进行了全基因组关联分析。通过与驯化基因组区域的比较，作者在驯化基因组区域内鉴定了25个与七种挥发性化合物相关联的数量性状位点，这与野生和栽培种桃树种挥发性化合物的差异相一致。最终，作者鉴定在先前已报道的一个QTL区域鉴定到了一个编码萜类合酶的基因，该基因与芳樟醇的生物合成相关。本文的研究结果揭示了本文所报道的新的桃树基因组对于桃的演化机制和基因鉴定研究具有非常重要的作用。此外，高质量的桃树基因组同样为未来的果树遗传改良提供了宝贵的信息。