Comparative genome sequencing of Drosophila pseudoobscura:: Chromosomal, gene, and cis-element evolution
Comparative genome sequencing of Drosophila pseudoobscura:: Chromosomal, gene, and cis-element evolution
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DOI：
10.1101/gr.3059305
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发表时间：
2005-01-01
期刊：
影响因子：
7
通讯作者：
Gibbs, RA
中科院分区：
文献类型：
--
作者：
Richards, S;Liu, Y;Gibbs, RA
我们已经对第二种果蝇的基因组进行了测序，并将其与主要模式生物黑腹果蝇的基因组序列进行了比较。在整个进化过程中，绝大多数果蝇基因都保留在同一条染色体臂上，但在每条染色体臂内，基因顺序都被广泛地重新洗牌，导致物种之间共享至少921个同线块。在A pseudobscura基因组中，在相邻同线块之间的许多连接处发现重复序列。对这个新的重复元件家族的分析表明，偏移元件之间的重组可能引起了许多旁着丝粒倒位，从而有助于D.拟暗纹谱系。基于序列相似性和同线性，10，516个推定的直向同源物已被鉴定为自伪暗/黑腹分歧以来在2500 - 5500万年（Myr）内保守的核心基因集。睾丸中表达的基因具有比全基因组平均值更高的氨基酸序列差异，这与性别特异性蛋白的快速进化一致。顺式调控序列在物种间比随机和邻近序列更为保守，但差异很小，这表明顺式调控元件的进化是灵活的。总的来说，重复介导的染色体重排的模式，以及雄性基因和顺式调控序列的高度共适应性，成为这些果蝇物种之间基因组分歧的重要主题。
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the A pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.