Luque T, Marfany G, Gonzàlez-Duarte R
Department de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain.
Mol Biol Evol. 1997 Dec;14(12):1316-25. doi: 10.1093/oxfordjournals.molbev.a025741.
Retrosequences, genes, and pseudogenes originated by retrotranscription are frequent components of vertebrate genomes, but they have only occasionally been described in invertebrates. In Drosophila, very few retrosequences have been reported, among them those of alcohol dehydrogenase (Adh) and phosphoglyceromutase (Pglym). Although 52 Adh gene sequences are available for comparison, Adh retrosequences have been described only in the sibling species D. teissieri and D. yakuba (melanogaster subgroup) and in D. subobscura (obscura subgroup). Here, we report the presence of Adh retrosequences in two closely related species of D. subobscura: D. madeirensis and D. guanche. Extensive sequence comparisons with their functional paralogs suggest separate retrotranscriptional events: one in the melanogaster subgroup in the ancestor of D. teissieri and D. yakuba, and the other in the obscura subgroup before the radiation of the lineages leading to D. subobscura, D. madeirensis, and D. guanche. In the former, the Adh retrotranscript originated a new expressed gene, named jingwei. However, in the obscura Adh retrosequences, retention of codon bias and higher Ks than Ka values, both distinctive evolutionary features supporting functionality, have to be considered together with a frameshift, premature stop codons, and other nucleotide substitutions, which, added to the lack of the original promoter elements, suggest that they are pseudogenes. At least two different Adh retrosequences have been characterized in each of the obscura species, and their phylogenetic analysis indicates that paralogs and their flanking genomic regions share a higher degree of similarity than orthologous sequences. Two alternative hypotheses could explain this current organization and structure: either a multiplication event occurred independently in each species, or gene conversion events should be invoked after a single duplication in the species ancestor. The significance of retrotranscriptional events in the evolution of invertebrate genomes is discussed.
反转录产生的反转序列、基因和假基因是脊椎动物基因组的常见组成部分，但在无脊椎动物中却鲜有报道。在果蝇中，报道的反转序列非常少，其中包括乙醇脱氢酶（Adh）和磷酸甘油变位酶（Pglym）的反转序列。尽管有52个Adh基因序列可供比较，但Adh反转序列仅在亲缘种拟果蝇和雅库布果蝇（黑腹果蝇亚组）以及暗果蝇（暗果蝇亚组）中被描述过。在此，我们报道在两种亲缘关系密切的暗果蝇物种：马德拉果蝇和加那利果蝇中存在Adh反转序列。与它们的功能旁系同源基因进行广泛的序列比较表明，存在独立的反转录事件：一次发生在拟果蝇和雅库布果蝇祖先所在的黑腹果蝇亚组中，另一次发生在导致暗果蝇、马德拉果蝇和加那利果蝇的谱系辐射之前的暗果蝇亚组中。在前者中，Adh反转录产物产生了一个新的表达基因，命名为经纬基因。然而，在暗果蝇的Adh反转序列中，密码子偏好性的保留以及Ks值高于Ka值（这两个独特的进化特征支持其功能性），必须与移码、提前终止密码子和其他核苷酸替换一起考虑，再加上缺乏原始启动子元件，这表明它们是假基因。在每个暗果蝇物种中至少鉴定出了两种不同的Adh反转序列，它们的系统发育分析表明旁系同源基因及其侧翼基因组区域比直系同源序列具有更高的相似性。两种替代假设可以解释当前的组织和结构：要么每个物种独立发生了倍增事件，要么在物种祖先单次复制后应调用基因转换事件。本文讨论了反转录事件在无脊椎动物基因组进化中的意义。
