Abstract

Using sequence-tagged DNA sequencing on the Roche 454 platform, we studied intragenomic polymorphism of one of the 35S rRNA regions (18S rDNA fragment–ITS1–fragment of 5.8S rDNA) in three hexaploid Avena species with karyotypes AACCDD and a tetraploid species A. insularis (AAСС or CCDD). Instead of expected 50% of C-variant ITS1 in A. insularis and 33% of C-variant ITS1 in hexaploids A. fatua, A. ludoviciana, and A. sterilis, the actual rate of C-subgenome specific ITSs comprised around 3.3% of rDNA in A. insularis and 1.4–2.4% of rDNA in hexaploid genomes. The 18S rDNA (fragment), ITS1 and 5.8S rDNA (small fragment) of the C-subgenome origin were 10 times more variable than the same sequences from the A-genome. Some of the C-subgenome sequences contained deletions, including deletions in the 18S rRNA coding region. The results of FISH hybridization with pTa71 and pTa794 confirm the fact that polyploids lost a significant part of the 35S rDNA and 5S rDNA obtained from a diploid ancestor with the CC karyotype. Our results show that the loss of the 35S rDNA of the C type occurs against the background of multiple single nucleotide polymorphisms (SNPs) and deletions accumulation in these sequences. The fact that all C-subgenome ITS1 sequences in the genomes of polyploids were represented by single (unique) copies might indicate that the appearance of multiple mutations in the “repressed” 35S rRNA loci was not accompanied by homogenization of rDNA. Hence, there is a reason to believe that the process of rDNA isogenization and the process of transcription/silencing are related phenomena.

中文翻译：

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多倍体Avena L的C亚基因组35S rRNA基因中的多重突变现象。

摘要

使用在Roche 454平台上进行序列标记的DNA测序，我们研究了三个六倍体Avena物种（核型AACCDD和一个四倍体物种A）中35S rRNA区域之一（18S rDNA片段– ITS1片段的5.8S rDNA片段）的基因组多态性。 insularis（AAСС或CCDD）。而不是预期的A. insularis中50％的C变异ITS1和六倍体A. fatua，A。ludoviciana和A中的33％C变异ITS1 。sterilis，C亚基因组特异ITS的实际比率约为insularis的rDNA的3.3％六倍体基因组中rDNA的1.4–2.4％。C亚基因组起源的18S rDNA（片段），ITS1和5.8S rDNA（小片段）的可变性是A基因组相同序列的10倍。一些C-亚基因组序列包含缺失，包括18S rRNA编码区中的缺失。FISH与pTa71和pTa794杂交的结果证实了以下事实：多倍体丢失了从CC型核型的二倍体祖先获得的35S rDNA和5S rDNA的很大一部分。我们的结果表明，C型35S rDNA的丢失是在多个单核苷酸多态性（SNP）和缺失积累在这些序列的背景下发生的。多倍体基因组中所有C-亚基因组ITS1序列均由单个（唯一）拷贝表示的事实可能表明，在“抑制”的35S rRNA基因座中出现多个突变并不伴随rDNA的均质化。因此，有理由相信rDNA的异化过程和转录/沉默过程是相关现象。