Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63
复制标题
两个优良籼稻品种珍山 97 和明徽 63 的参考基因组之间存在广泛的序列差异
DOI：
10.1073/pnas.1611012113
复制
发表时间：
2016-08-30
影响因子：
11.1
通讯作者：
Zhang, Qifa
中科院分区：
文献类型：
--
作者：
Zhang, Jianwei;Chen, Ling-Ling;Zhang, Qifa
意义籼稻占全球水稻总产量的70%，具有高度的遗传多样性，可分为两大品种群，分别在中国和东南亚地区独立培育和广泛栽培。在这里，我们生成了两个优质水稻品种珍珊97和明恢63的高质量基因组序列，这两个品种代表了两个籼稻群体和一个领先杂交水稻的亲本。比较分析揭示了这两个基因组之间广泛的结构差异和它们的杂交转录组的互补性。这些发现对理解具有复杂基因组的生物体的种内变异具有普遍意义。这两个基因组的可获得性将为未来基于基因组的水稻探索奠定基础，实现基本和应用目标。亚洲栽培稻由两个亚种组成：水稻亚种。和栽培稻亚种。日本菜。尽管籼稻占全球水稻总产量的70%以上，并且在遗传上更加多样化，但高质量的籼稻参考基因组尚未公布。我们对两个籼稻品系珍山97(ZS97)和明恢63(MH63)进行了基于图谱的测序，这两个品系代表了两个主要的籼亚种品种群，是中国一个优秀杂交种的亲本。基因组序列被组装成237(ZS97)和181(MH63)重叠群，准确率为99.99%，覆盖了估计基因组大小的90.6%和93.2%。对这两个籼稻基因组的比较分析发现了惊人的结构差异，特别是在倒位、易位、存在/缺失变异和节段复制方面。大约42%的非转座元件相关基因在两个基因组之间是相同的。对三种组织的转录组分析表明，杂交种比亲本多表达1,059-2,217个基因，并且由于亲本基因组的差异，杂交种中表达的基因更加多样化。两个高质量的水稻亚种参考基因组的公开可用将对植物生物学和作物遗传改良产生广泛的影响。
Significance Indica rice accounts for >70% of total rice production worldwide, is genetically highly diverse, and can be divided into two major varietal groups independently bred and widely cultivated in China and Southeast Asia. Here, we generated high-quality genome sequences for two elite rice varieties, Zhenshan 97 and Minghui 63, representing the two groups of indica rice and the parents of a leading rice hybrid. Comparative analyses uncovered extensive structural differences between the two genomes and complementarity in their hybrid transcriptome. These findings have general implications for understanding intraspecific variations of organisms with complex genomes. The availability of the two genomes will serve as a foundation for future genome-based explorations in rice toward both basic and applied goals. Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059–2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.