Langille Morgan G I, Clark Denise V
Department of Biology, University of New Brunswick, Fredericton, Canada NB E3B 6E1.
Genomics. 2007 Sep;90(3):334-43. doi: 10.1016/j.ygeno.2007.06.001. Epub 2007 Jul 12.
Genes arising by retrotransposition are always different from their parent genes from the outset. In addition, the cDNA must insert into a region that allows expression or it will become a processed pseudogene. We sought to determine whether this class of gene duplication differs from other gene duplications based on functional criteria. Using amino acid sequences from Drosophila melanogaster, we identified retroduplicated gene pairs at various levels of sequence identity. Analysis of gene ontology annotations showed some enrichment of retroduplications in the cellular physiological processes class. Retroduplications show a higher level of nucleotide substitution than other gene duplications, suggesting a higher rate of divergence. Remarkably, analysis of microarray data for gene expression during embryogenesis showed that parent genes are more highly expressed relative to their retroduplicated copies, tandem duplications, and all genes. Furthermore, an expressed sequence tag library representation shows a broader distribution for parent genes than for all other genes and, as found previously by others, retroduplicated gene transcripts are found most abundantly in testes. Therefore, in examining retroduplicated gene pairs, we have found that parent genes of retroduplications are also a distinctive class in terms of transcript expression levels and distribution.
通过逆转座产生的基因从一开始就与其亲本基因不同。此外，cDNA必须插入到允许表达的区域，否则它将成为一个加工假基因。我们试图根据功能标准确定这类基因复制是否与其他基因复制不同。利用黑腹果蝇的氨基酸序列，我们鉴定了不同序列同一性水平的逆转座复制基因对。基因本体注释分析表明，逆转座复制在细胞生理过程类别中有所富集。逆转座复制比其他基因复制表现出更高水平的核苷酸替代，表明其分化速率更高。值得注意的是，对胚胎发育过程中基因表达的微阵列数据分析表明，相对于它们的逆转座复制拷贝、串联重复以及所有基因，亲本基因的表达水平更高。此外，一个表达序列标签文库的表现表明，亲本基因的分布比所有其他基因更广泛，并且，正如其他人之前所发现的，逆转座复制基因转录本在睾丸中最为丰富。因此，在研究逆转座复制基因对时，我们发现，就转录本表达水平和分布而言，逆转座复制的亲本基因也是一个独特的类别。
