The pomegranate (Punica granatum L.) genome

石榴（学名：Punica granatum L.），是一种多年生、古老的药用水果作用，其天然分布于中亚地区。据记载，石榴于唐朝通过丝绸之路传入中国，之后在中国得到广泛的栽培。早期分类学者将石榴属归入千屈菜科，但石榴科子房下位，有多数雄蕊从子房上方的肥厚花托内发出，显然和千屈菜科不同，现时学者均将此属成独立的科，和桃金娘科、千屈菜科等同列入桃金娘目（老板提供^-^）。石榴主要的水果产品就是石榴，其具有非常丰富的营养价值和宝贵的药用价值。石榴果实成熟时的颜色变化是基础科学研究中的一个重要研究方向；另外还有就是石榴果实含有丰富的鞣花单宁类化合物，这一类物质的生物合成也是石榴研究的主要方向。石榴果实中最主要的生物活性物质是鞣花酸（ellagic acid）和石榴皮鞣素（punicalin），但石榴果汁中的鞣花酸被证明在体内不会在人体血液中积累，因此不具有直接的生物活性。然而，石榴具有一种特有的鞣花单宁（ellagitannin）类生物活性物质叫做安石榴甙（punicalagin），而安石榴甙可以在肠道中水解，释放出鞣花酸，其进一步会被肠道微生物代谢形成一种叫做urolithin的代谢产物，该代谢产物在16年的Nature Medicine一篇文章中被证明能够改善线粒体和肌肉功能、提高衰老过程中肌肉力量和耐力，因此石榴中安石榴甙的生物合成也逐渐受到重视。

The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis

Pomegranate (Punica granatum L.; 石榴) is a perennial fruit crop grown since ancient times that has been planted worldwide and is known for its functional metabolites (代谢产物), particularly punicalagins (安石榴苷). We have sequenced and assembled the pomegranate genome with 328 Mb anchored into nine pseudo-chromosomes and annotated 29,229 gene models. A Myrtales (桃金娘目) lineage-specific whole-genome duplication (WGD) event was detected that occurred in the common ancestor before the divergence of pomegranate and Eucalyptus. Repetitive sequences accounted for 46.1% of the assembled genome. We found that the integument (珠被) development gene INNER NO OUTER (INO) was under positive selection and potentially contributed to the development of the fleshy (肉质的) outer layer of the seed coat (种皮), an edible (可食用的) part of pomegranate fruit. The genes encoding the enzymes for synthesis and degradation of lignin, hemicelluloses (半纤维素), and cellulose were also differentially expressed between soft- and hard-seeded varieties, reflecting differences in their accumulation in cultivars differing in seed hardness. Candidate genes for punicalagin biosynthesis were identified and their expression patterns indicated that gallic acid (没食子酸) synthesis in tissues could follow different biochemical pathways. The genome sequence of pomegranate provides a valuable resource for the dissection of many biological and biochemical traits and also provides important insights for the acceleration of breeding. Elucidation (阐明) of the biochemical pathway(s) involved in punicalagin biosynthesis could assist breeding efforts to increase production of this bioactive compound (生物活性化合物).

石榴是多年生的水果作物，其栽培历史悠久，营养价值高，尤其是代谢产物安石榴苷。本文作者对石榴的核基因组进行了测序，共组装出328 Mb锚定到9条假染色体上，并注释了29,229个基因模型。作者在石榴基因组中鉴定出一次桃金娘目特有的全基因组复制事件，该复制事件发生时间先于石榴与桉属植物的分化。石榴基因组中重复序列占了46.1%。作者发现珠被发育基因INO在进化中受到了正选择，可能有助于石榴可食用部分，即种皮肉质外层的形成。在软核和硬核石榴品种中，木质素、半纤维素和纤维素合成和降解相关基因有表达差异，显示在不同硬度种子的石榴品种中木质素、半纤维素和纤维素的积累过程不同。作者还鉴定了安石榴苷生物合成相关候选基因，这些基因的表达模式显示没食子酸生物合成可能紧跟不同的生化通路。石榴的基因组测序为石榴中许多生物或生化性状的鉴定提供了宝贵的基因组序列资源，也为石榴将来的加速育种提供了分子基础。涉及到安石榴苷合成生物通路的阐明能够为以提高该生化活性化合物产量为目的的石榴育种提供可能。

通讯：徐义流

doi: 10.1111/tpj.13625

First Published date: 3 August, 2017

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

Pomegranate (Punica granatum L.) has an ancient cultivation history, and has become an emerging profitable (可赚钱的) fruit crop due to its attractive features such as the bright red (鲜红) appearance and the high abundance of medicinally valuable (药用价值) ellagitannin-based compounds (鞣花单宁类化合物) in its peel (果皮) and aril (假种皮). However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2,177 scaffolds with an N50 size of 1.7 Mb, and contains 30,903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family (千屈菜科) rather than the monogeneric Punicaceae family (石榴科), and comparative analyses showed that pomegranate and Eucalyptus grandis shares the paleotetraploidy event (古四倍化事件). Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the color formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.

石榴是一种古老的栽培作物，并由于其果实具有鲜红的外表，果皮和果肉更是富含药用价值的鞣花单宁类化合物，石榴正越来越成为经济效益高的水果作物。然而，由于缺少基因组信息，严重限制了石榴果实性状的遗传学基础研究。本文报道了石榴高质量基因组草图，组装大小约274-Mb，占预估基因组大小81.5%，由2,177个scaffold构成，scaffold N50大小为1.7 Mb，共注释出30,903个基因。进化分析显示石榴相对于之前的分类属于单属科石榴科，更有可能是千屈菜科中的一个属。比较基因组分析显示，石榴和巨桉共享了一次古四倍化事件。整合基因组和转录组的数据分析，本文为石榴果实中的鞣花单宁类化合物的生物合成、石榴果实发育过程中的果皮和假种皮的颜色变化，以及石榴特色的胚珠发育的分子机理提供了一些新的见解。本文报道的石榴基因组将为进一步拓宽我们对石榴一些特有的生物学问题的理解，同时也将促进石榴生物学和作物育种的研究。

通讯：苑兆和 (http://linxue.njfu.edu.cn/info.php?cid=117)

个人简介： 1983年毕业于南京林业大学。1994年1月至1997年1月先后在美国华盛顿州立大学灌溉农业研究与推广中心和马里兰大学园艺系做访问学者。

doi: 10.1111/pbi.12875

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