Eickbush D G, Lathe W C, Francino M P, Eickbush T H
Department of Biology, University of Rochester, New York 14627, USA.
Genetics. 1995 Feb;139(2):685-95. doi: 10.1093/genetics/139.2.685.
The non-long-terminal repeat retrotransposable elements, R1 and R2, insert at unique locations in the 28S ribosomal RNA genes of insects. Based on the nucleotide sequences of these elements in the eight members of the melanogaster species subgroup of the genus Drosophila, they have been maintained by vertical germline transmission for the 17-20 million year history of this subgroup. The stable inheritance of R1 and R2 within these species has enabled a determination of their nucleotide substitution rates. The sequence of the R1 and R2 elements from D. ambigua, a member of the obscura species group, has also been determined to enable an extrapolation of this rate over an estimated 45-60 million years. The mean rate of substitutions at synonymous sites (Ks) was 6.6 and 9.6 times the rate at replacement sites (Ka) in the R1 and R2 elements, respectively. Both elements appear to have been under selective pressure to maintain their open reading frames and thus their ability to retrotranspose for most of their evolution in these lineages. Using the rate of change at synonymous sites (Ks) as the best indicator of the nucleotide substitution rate, the mean Ks values for R1 and R2 were 2.3 and 2.2 times that of the alcohol dehydrogenase (Adh) genes. However, this faster rate is a result of the lower codon usage bias of R1 and R2 compared with that of Adh. When the Ks rates of R1 and R2 were compared with that of a larger number of nuclear genes available from at least two of the nine species under investigation, R1 and R2 were found to evolve in most lineages at rates similar to that of nuclear genes with low codon bias. The ability of R1 and R2 to maintain their presence in this species subgroup by retrotransposition while exhibiting rates of nucleotide evolution similar to nuclear genes suggests these transposition events are rare or not as error prone as that of retroviruses.
非长末端重复逆转座子元件R1和R2插入昆虫28S核糖体RNA基因的独特位置。根据果蝇属黑腹果蝇物种亚组八个成员中这些元件的核苷酸序列，在该亚组1700万至2000万年的历史中，它们通过垂直种系传递得以保留。这些物种中R1和R2的稳定遗传使得能够确定它们的核苷酸替代率。已确定了果蝇属 obscura 物种组成员 D. ambigua 的R1和R2元件序列，以便在估计的4500万至6000万年时间内推断该速率。在R1和R2元件中，同义位点（Ks）的平均替代率分别是替换位点（Ka）的6.6倍和9.6倍。在这些谱系的大部分进化过程中，这两个元件似乎都受到了选择压力，以维持其开放阅读框，从而保持其逆转座能力。以同义位点的变化率（Ks）作为核苷酸替代率的最佳指标，R1和R2的平均Ks值分别是乙醇脱氢酶（Adh）基因的2.3倍和2.2倍。然而，这种更快的速率是由于R1和R2与Adh相比密码子使用偏好较低所致。当将R1和R2的Ks速率与从所研究的九个物种中的至少两个物种获得的大量核基因的Ks速率进行比较时，发现R1和R2在大多数谱系中的进化速率与密码子偏好较低的核基因相似。R1和R2通过逆转座在该物种亚组中保持存在的能力，同时表现出与核基因相似的核苷酸进化速率，这表明这些转座事件很少见，或者不像逆转录病毒那样容易出错。
