A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences
A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences
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DOI：
10.1007/s12042-014-9139-3
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发表时间：
2014-06-01
影响因子：
2
通讯作者：
Aitken, Karen S.
中科院分区：
文献类型：
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作者：
Berkman, Paul J.;Bundock, Peter C.;Aitken, Karen S.
甘蔗(Saccharum spp.)是一种对粮食和燃料都具有重大国际意义的作物，但其高度多倍体的性质对其遗传组成的研究提出了挑战。产生甘蔗全基因组序列的努力正在进行中，但与此同时，由于缺乏可用于生理特性的基因组序列资源，作物改良努力在一定程度上受到了限制。低覆盖率的调查序列数据被生成并组合成6个甘蔗基因型，代表了来自世界各地的一系列重要的甘蔗品种。这些数据被用来研究叶绿体基因组序列的重复序列和变异的组成，以及组装成一个聚集的单倍体基因组序列，用于基因型之间的多态比较。在这些数据中分析的基因组间多态几乎有一半(47%)是多等位基因变异，不能应用于传统的有/无标记分析，这表明需要新的方法来更好地了解和获取甘蔗属内的遗传多样性。这些结果支持先前的断言，即自发性链球菌的重复率较低(曼德勒的k-MERS重复频率为62%，而IJ76-514为65%)，但多态程度较高(曼德勒为17%的多等位基因，而IJ76-514为10%)，而药用沙门氏菌的杂交后代介于两者之间。然而，与先前的分析相反，自然链球菌的单倍体基因组大小似乎并没有像预期的那样与药用链球菌的基因组大小有显著差异。在没有单倍体或多倍体基因组序列的情况下，这种基因组调查组合将是甘蔗基因组学非常有用的资源，并将根据要求提供。
Sugarcane (Saccharum spp.) is a crop of substantial international significance for both food and fuel, however its highly polyploid nature challenges investigation of its genetic composition. Efforts to generate the full sugarcane genome sequence are underway, however in the meantime crop improvement efforts are somewhat limited by the lack of genome sequence resources available for physiological characterization. Low-coverage survey sequence data was generated and assembled for six sugarcane genotypes representing a range of significant S. spontaneum, S. officinarum, and S. hybrid cultivar accessions from around the world. These data were explored to investigate the composition of repetitive sequences and variations in chloroplast genome sequence, as well as assembled into a conglomerate monoploid genome sequence for polymorphism comparison between the genotypes. Almost half (47 %) of the inter-genomic polymorphisms analysed in these data represented poly-allelic variations which cannot be applied in traditional present/absent marker analysis, suggesting that new approaches are required to better understand and access genetic diversity within the Saccharum genus. These results support previous assertions that S. spontaneum is both less repetitive (62 % repetitive k-mers in Mandalay vs. 65 % in IJ76-514) and more highly polymorphic (17 % poly-alleles in Mandalay vs. 10 % poly-alleles in IJ76-514) than S. officinarum, with S. hybrids being intermediate between the two. However, contrary to previous analysis the monoploid genome size of S. spontaneum does not appear to differ significantly from that of S. officinarum as had been expected. This genomic survey assembly will be a very useful resource for sugarcane genomics in the absence of a monoploid or polyploid genome sequence, and will be made available upon request.