Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
复制标题
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
DOI：
10.1371/journal.pbio.0050310
复制
发表时间：
2007-11-06
期刊：
影响因子：
9.8
通讯作者：
Langley, Charles H.
中科院分区：
文献类型：
--
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
种群遗传学观点认为，形成基因组变异的过程只能通过同时调查密切相关物种内部和之间的序列多态和分歧来揭示。在这里，我们提出了一种基于多个近交系的全基因组鸟枪测序的模拟果蝇的群体遗传学分析，并将所得数据与密切相关的物种黑腹果蝇和雅库巴果蝇的基因组组合进行比较。我们发现了以前未知的、沿染色体臂的多态和分歧的大规模波动，而X染色体上的多态显著减少，分歧更快。我们生成了一份受适应性进化影响的仿生杜氏菌基因组功能元件的综合清单。最后，我们描述了编码和非编码序列的碱基组成的基因组模式。这些结果为控制果蝇基因组的多态和分化的遗传和生物学机制提出了几个新的假说，并为研究拟果蝇的适应性进化和功能变异提供了丰富的资源。种群基因组学研究紧密相关物种内部和之间的全基因组序列变化模式，可以全面地了解突变、重组、自然选择和遗传漂移在进化中的相对重要性。它还可以提供对生物的生物属性的基本见解，这些属性是由适应性进化具体塑造的。生成种群基因组数据集的一种方法是将全基因组鸟枪项目的DNA序列与标准参考序列进行比对。我们使用这种方法对模拟果蝇的多态和分化进行了全基因组分析，模拟果蝇是模式系统黑腹果蝇的近亲。我们发现，基因组中的多态和分歧在很大程度上是波动的，这些波动可能是由自然选择而不是突变率的差异来解释的。我们的分析表明，适应性蛋白质进化是常见的，通常与生物过程有关，这些过程可能与基因表达、染色体生物学和生殖有关。本文提出的方法将在未来对包括人类在内的其他系统的种群基因组变异进行分析时具有广泛的适用性。来自多个模拟果蝇品系的低覆盖率基因组序列提供了第一个关于果蝇多态和分歧的全面视图。
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans. Population genomics, the study of genome-wide patterns of sequence variation within and between closely related species, can provide a comprehensive view of the relative importance of mutation, recombination, natural selection, and genetic drift in evolution. It can also provide fundamental insights into the biological attributes of organisms that are specifically shaped by adaptive evolution. One approach for generating population genomic datasets is to align DNA sequences from whole-genome shotgun projects to a standard reference sequence. We used this approach to carry out whole-genome analysis of polymorphism and divergence in Drosophila simulans, a close relative of the model system, D. melanogaster. We find that polymorphism and divergence fluctuate on a large scale across the genome and that these fluctuations are probably explained by natural selection rather than by variation in mutation rates. Our analysis suggests that adaptive protein evolution is common and is often related to biological processes that may be associated with gene expression, chromosome biology, and reproduction. The approaches presented here will have broad applicability to future analysis of population genomic variation in other systems, including humans. Low-coverage genome sequences from multiple Drosophila simulans strains provide the first comprehensive view of polymorphism and divergence in the fruit fly.
登录
查看更多内容
影响因子：
3.8
作者：
BABAAISSA, F;SOLIGNAC, M;DAVID, JR
通讯作者：
DAVID, JR
影响因子：
1.5
作者：
AVERY, PJ
通讯作者：
AVERY, PJ
影响因子：
10.7
作者：
Bierne, N;Eyre-Walker, A
通讯作者：
Eyre-Walker, A
影响因子：
7
作者：
Bray, N;Pachter, L
通讯作者：
Pachter, L
影响因子：
3.4
作者：
BRESSAC, C;ROUSSET, F
通讯作者：
ROUSSET, F