我所曹尚银研究员课题组破译软籽石榴‘突尼斯’全基因组

　　近日，中国农业科学院郑州果树研究所曹尚银研究员课题组在国际生物技术学术期刊Plant Biotechnology Journal在线发表了题为“The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars”的研究论文，该研究为解析软籽和硬籽石榴品种分化遗传机制提供了基础。

　　石榴 (Punica granatum L.) 是一古老的落叶灌木果树树种，栽培历史悠久。石榴被誉为“生命之果”，其果皮、果肉以及种子均含有丰富的类黄酮、多酚、花青素等抗氧化物质，有利于预防高血脂、高血压、HIV、传染性疾病、冠心病、前列腺癌症等疾病。尤其是软籽石榴品种，籽粒硬度小，食用时易于吞咽，避免了营养的流失；此外，软籽石榴市场售价通常是普通品种的2–4倍，是广大果农脱贫致富的良果佳品。‘突尼斯’石榴是目前国内广泛栽培的软籽品种，由中国林业部1986年从突尼斯国引进。与硬籽石榴相比，软籽石榴的不抗冻，严重威胁和制约了软籽石榴产业健康持续发展。高质量的基因组图谱为软籽石榴遗传改良研究奠定了重要基础。

　　该研究基于二代和三代测序获得了软籽石榴‘突尼斯’高质量基因组序列，基因组大小为320.31 Mb，Contig N50为4.49 Mb，注释了33,594个基因。采用Hi-C光学技术结合遗传图谱将97.76%的序列组装到了8对染色体上。与现有的‘泰山红’石榴基因组相比，‘突尼斯’多组装出了46.01Mb序列，Contig N50的平均长度提升了46倍，在组装完整度及精确度上都得到了极大地提升。

　　比较基因组学研究表明，软籽‘突尼斯’基因组和硬籽‘泰山红’、‘大笨籽’基因组间存在着大量的SNP和InDel变异。对26个石榴品种进行群体遗传学分析表明，软籽石榴群体和硬籽石榴群体间存在着大量的受选择位点。尤其是Chr1上，存在着高达26.2Mb的受选择区段。基因注释信息表明，与基因组变异及选择信号相关的基因潜在地影响着石榴硬籽和软籽特性分化。

　　本论文的通讯作者为曹尚银研究员，第一作者为骆翔博士。本研究得到了中国农业科学院科技创新工程（CAAS-ASTIP-2015-ZFRI）以及国家科技基础性工作专项重点项目（2012FY110100）的资助。

　　图1 基因组组装和分化遗传因子

　　Figure1 Genome assembly and genetic factors associated to the genetic divergence between soft- and hard-seeded cultivars

　　图2 突尼斯石榴

　　Figure 2 ‘Tunisia’ cultivar

　　The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars

　　The new article that assembled the soft-seeded pomegranate ‘Tunisia’ genome was published on Plant Biotechnology Journal at September 24, 2019. This study provides new insights into the genetic divergence between soft- and hard-seeded cultivars in pomegranate, which is helpful for future molecular improvement.

　　Pomegranate (Punica granatum L.) is an important edible fruit tree species native to central Asia. The fruit has gained widespread popularity because of its functional and nutraceutical properties. The properties of pomegranate juices, seeds, and extracts are potentially beneficial for treating cardiovascular disease, diabetes, and prostate cancer. Traditional hard-seeded pomegranate varieties are well adapted to the cold environment, whereas the soft-seeded varieties have become popular with consumers as their fruits are easily swallowed. Additionally, soft-seeded varieties fetch high price in the market as compared to hard seeded. To date, ‘Tunisia’ has been the only one commercial variety introduced from Tunisia since 1986. The problem of single variety and depression seriously restricts the development of pomegranate industry. Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of pomegranate.

　　In this study, we integrated single-molecule sequencing and high-throughput chromosome conformation capture techniques to produce a high-quality and long-range contiguity chromosome-scale genome assembly of the soft-seeded pomegranate cultivar‘Tunisia’. The genome covers 320.31 Mb (contig N50 = 4.49 Mb) and includes 33,594 protein-coding genes. 97.76% (313.13 Mb) of the assembly was anchored on eight chromosomes. The length of contig N50 for the new‘Tunisia’reference genome was 46-fold greater than that for the recently published‘Taishanhong’genomes.

　　Comparative genomic analyses revealed many genetic differences between soft- and hard-seeded pomegranate varieties. Re-sequenced 26 pomegranate varieties revealed a set of selective loci. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Gene annotation indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft- and hard-seeded pomegranate varieties.

　　The corresponding author and first author Prof. Shangyin Cao and PhD Xiang Luo, respectively. This project was funded by the Key Project of the National Science and Technology Basic Work of China (2012FY110100) and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2015-ZFRI).

　　The URL for this article should be: https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.13260 

　　By Xiang Luo

　　Email: tjaulx@126.com