Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
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DOI：
10.1186/1471-2229-7-44
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发表时间：
2007-08-16
影响因子：
5.3
通讯作者：
Comai, Luca
中科院分区：
文献类型：
--
作者：
Davison, Jerry;Tyagi, Anand;Comai, Luca
背景：真核生物个体基因组的组成及其在一个物种内的变异仍然很难确定。即使是一个测序的基因组，如模式植物拟南芥登录Col-0，大阵列的异染色质重复序列是不完全测序的，与不确定的大小的差距坚持在them.Results：使用地理上分离的种群的A。thaliana，我们分析了异染色质重复序列的变化，使用两种独立的方法，并确定了显着的多态性，与变化多达两个因素在着丝粒180 bp重复，在45 S rDNA阵列和Athila retroelements。在通过流式细胞术测量的具有最高基因组大小的加入中，洛-0，我们发现5S RNA基因拷贝相对于Col-0增加了两倍以上; 5S探针荧光原位杂交的结果与5S位点处洛-0和Col-0之间存在大小多态性一致。洛-0和Col-0的比较基因组杂交结果不支持蛋白质编码基因拷贝数的连续变异，其规模需要解释其观察到的基因组大小差异。我们开发了一个计算数据模型来测试我们测量的重复片段的变异是否可以解释流式细胞仪测定的不同基因组大小，并发现这种关系可以解释基因组大小的变异的50%左右的acces.Conclusion：我们的分析是一致的，大量的重复数多态性的5S和45 S核糖体基因之间的acces. Conclusion。thaliana.差异也建议为着丝粒和近着丝粒重复。我们的分析还指出了测量基因组重复部分的困难，并建议除了流式细胞术测量外，还应寻求基因组大小的独立验证。
Background: The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them.Results: Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions.Conclusion: Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.