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我所曹尚银研讨员课题组破译软籽石榴‘突尼斯’全基因组

泉源:线赌博平台开户网站干果种质改进 作者:骆翔 2019-10-09 10:36:00 阅读量:

  克日,中国农业迷信院线赌博平台开户网站曹尚银研讨员课题组在国际生物技能学术期刊Plant Biotechnology Journal在线宣布了题为“The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars”的研讨论文,该研讨为剖析软籽和硬籽石榴种类分解遗传机制提供了根底。

  石榴 (Punica granatum L.) 是一陈旧的落叶灌木果树树种,种植汗青久长。石榴被誉为“生命之果”,其果皮、果肉以及种子均含有丰厚的类黄酮、多酚、花青素等抗氧化物质,有利于防备高血脂、高血压、HIV、感染性疾病、冠心病、前线腺癌症等疾病。尤其是软籽石榴种类,籽粒硬度小,食用时易于吞咽,防止了养分的流失;别的,软籽石榴市场售价通常是平凡种类的2–4倍,是广阔果农脱贫致富的良果佳品。‘突尼斯’石榴是现在国际普遍种植的软籽种类,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,严峻要挟和制约了软籽石榴财产安康继续开展。高质量的基因组图谱为软籽石榴遗传改进研讨奠基了紧张根底。

  该研讨基于二代和三代测序取得了软籽石榴‘突尼斯’高质量基因组序列,基因组巨细为320.31 Mb,Contig N50为4.49 Mb,正文了33,594个基因。接纳Hi-C光学技能联合遗传图谱将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的均匀长度提拔了46倍,在组装完好度及准确度上都失掉了极大地提拔。

  比拟基因组学研讨标明,软籽‘突尼斯’基因组和硬籽‘泰山红’、‘大笨籽’基因组间存在着少量的SNP和InDel变异。对26个石榴种类停止群体遗传学剖析标明,软籽石榴群体和硬籽石榴群体间存在着少量的受选择位点。尤其是Chr1上,存在着高达26.2Mb的受选择区段。基因正文信息标明,与基因组变异及选择信号相干的基因潜伏地影响着石榴硬籽和软籽特性分解。

  本论文的通讯作者为曹尚银研讨员,第一作者为骆翔博士。本研讨失掉了中国农业迷信院科技创新工程(CAAS-ASTIP-2015-ZFRI)以及国度科技根底性任务专项重点项目(2012FY110100)的赞助。

  

  

  图1 基因组组装和分解遗传因子

  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