Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
Heredity (Edinb). 2010 Nov;105(5):463-72. doi: 10.1038/hdy.2009.192. Epub 2010 Feb 17.
After polyploid formation, retention or loss of duplicated genes is not random. Genes with some functional domains are convergently restored to 'singleton' state after many independent genome duplications, and have been referred to as 'duplication-resistant' (DR) genes. To further explore the timeframe for their restoration to the singleton state, 27 cotton homologs of genes found to be 'DR' in Arabidopsis were selected based on diagnostic Pfam domains. Their copy numbers were studied using southern hybridization and sequence analysis in five tetraploid species and their ancestral A and D genome diploids. DR genes had significantly lower copy number than gene families hybridizing to randomly selected cotton ESTs. Three DR genes showed complete loss of D genome-derived homoeologs in some or all tetraploid species. Prior analysis has shown gene loss in polyploid cotton to be rare, and herein only one randomly selected gene showed loss of a homoeolog in only one of the five tetraploid species (Gossypium mustelinum). BAC sequencing confirmed two cases of gene loss in tetraploid cotton. Divergence among 5' sequences of DR genes amplified from G. arboreum, G. raimondii, and Gossypioides kirkii was correlated with gene copy number. These results show that genes containing Pfam domains associated with duplication resistance in Arabidopsis have also been preferentially restored to low copy number after a more recent polyploidization event in cotton. In tetraploid cotton, genes from the progenitor D genome seem to experience more gene copy number divergence than genes from the A genome. Together with D subgenome-biased alterations in gene expression, perhaps gene loss may contribute to the relatively larger portion of quantitative trait variation attributable to D than A subgenome chromosomes of tetraploid cotton.
多倍体形成后，重复基因的保留或丢失并非随机。具有某些功能结构域的基因在经历多次独立的基因组加倍后，会被收敛性地恢复到“单体”状态，这些基因被称为“抗重复（DR）”基因。为了进一步探索它们恢复到单体状态的时间框架，我们根据诊断 Pfam 结构域，从拟南芥中发现的“DR”基因中选择了 27 个棉花同源基因。我们使用Southern 杂交和序列分析，研究了这 27 个基因在 5 个四倍体物种及其祖先 A 和 D 基因组二倍体中的拷贝数。DR 基因的拷贝数明显低于与随机选择的棉花 EST 杂交的基因家族。在一些或所有四倍体物种中，有 3 个 DR 基因完全丢失了 D 基因组衍生的同系物。之前的分析表明，多倍体棉花中的基因丢失很少见，而在此，只有一个随机选择的基因在 5 个四倍体物种中的一个物种（棉叶刺棉）中丢失了一个同系物。BAC 测序证实了在四倍体棉花中发生了两个基因丢失的情况。从亚洲棉、雷蒙德氏棉和棉叶刺棉中扩增的 DR 基因的 5'序列之间的差异与基因拷贝数相关。这些结果表明，在棉花最近的一次多倍化事件后，含有与拟南芥抗重复相关 Pfam 结构域的基因也被优先恢复到低拷贝数。在四倍体棉花中，来自祖先 D 基因组的基因似乎比来自 A 基因组的基因经历了更多的基因拷贝数变异。与 D 亚基因组偏向的基因表达改变一起，也许基因丢失可能导致四倍体棉花的 D 亚基因组染色体比 A 亚基因组染色体对数量性状变异的贡献相对更大。
