Department of Mathematics and Statistics, University of Ottawa, Ottawa K1N 6N5, Canada.
BMC Genomics. 2010 May 19;11:313. doi: 10.1186/1471-2164-11-313.
Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement.
We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome.
Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of transcriptional co-regulation, dosage sensitivity or other functional interaction constraining the reduction process. These constraints and their evolution over time show a consistent pattern across evolutionary domains and a highly reproducible pattern, as replicates, for the several descendants of a single WGD.
通过转座元件的复制或增殖进行基因组扩增，其对应物是通过消除 DNA 或基因失活进行的基因组减少。DNA 随机长度片段的缺失或一次失活一个基因是否是主要原因仍存在争议。全基因组复制 (WGD) 后的减少代表了基因组成的不可避免的崩溃。
我们比较了来自六个真核生物 WGD 事件 20-450 Mya 的十五个基因组。我们通过比较重复片段中减少的直系同源基因对的分布来描述随时间的崩溃。同一 WGD 事件的后代基因组作为重复样本。除了一些连续的同源基因对的抗性区域外，减少的直系同源基因对的选择是随机的。对于那些减少的直系同源基因对，保守拷贝往往集中在一条染色体上。
减少抗性同源基因对的连续区域和单拷贝基因的连续区集中在一条染色体上，这两个证据都表明转录共调控、剂量敏感性或其他功能相互作用限制了减少过程。这些限制及其随时间的进化在进化领域中表现出一致的模式，并且对于单个 WGD 的几个后代，表现出高度可重复的模式。
