Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
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DOI：
10.1371/journal.pgen.1003129
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Bergman CM
中科院分区：
文献类型：
--
作者：
Richardson MF;Weinert LA;Welch JJ;Linheiro RS;Magwire MM;Jiggins FM;Bergman CM
沃尔巴克氏体是母系遗传的共生细菌，通常在节肢动物中发现，它们能够操纵宿主的繁殖，以最大限度地传播。沃尔巴克氏体等内共生菌的进化史可以通过整合沃尔巴克氏体和宿主线粒体基因组序列变异模式在自然种群中的感染状态信息来揭示。在这里，我们使用来自北美、欧洲和非洲的290个黑腹果蝇的全基因组重测序数据来预测沃尔巴克氏体感染状态，估计相对细胞质基因组拷贝数，并重建沃尔巴克氏体和线粒体基因组序列。总体而言，我们的计算机分析管道预测63%的果蝇菌株感染沃尔巴克氏体，与诊断PCR检测的感染状态一致性达99%。完整的沃尔巴克氏体和线粒体基因组显示出一致的系统发育，这与沃尔巴克氏体通过母体细胞质的严格垂直传播和不完全传播相一致。贝叶斯系统发育分析显示，所有沃尔巴克氏体和黑腹龙线粒体基因组最近的共同祖先可以追溯到大约8000年前。我们发现了最近全球替代祖先沃尔巴克氏体和mtDNA谱系的证据，但我们的数据表明，衍生的wMel谱系出现在几千年前，而不是像之前提出的那样出现在20世纪。我们的数据还提供了证据，表明这一全球替代事件是不完整的，很可能是自非洲外迁徙以来发生的几个类似的不完整替代事件之一，这些事件使黑腹龙得以在全球栖息地定居。本研究为黑腹菌与沃尔巴克氏菌共生的进化模式和时间动态提供了完整的基因组分析，为进一步分析沃尔巴克氏菌对宿主生物学的影响提供了重要的资源。宿主-微生物相互作用在许多生物的生理、发育和生态学中起着重要作用。研究宿主及其微生物共生体如何随着时间的推移共同进化，对于理解微生物对宿主生物学的影响至关重要。随着高通量测序技术的出现，现在可以获得宿主及其相关微生物的完整基因组信息。在这里，我们使用来自果蝇果蝇约300株的全基因组序列来揭示这种模式物种及其细胞内细菌共栖体沃尔巴克氏体的进化史。本研究的主要发现是：黑腹龙种的沃尔巴克氏体是严格通过卵子遗传的，没有其他物种水平转移的证据，沃尔巴克氏体和线粒体基因组的谱系实际上是相同的，沃尔巴克氏体和线粒体基因组都显示了最近不完整的全球替代事件的证据，这在北美、欧洲和非洲留下了残余的谱系。我们还利用沃尔巴克氏体和线粒体基因组具有相同谱系的事实来估计沃尔巴克氏体的分子进化速度，这使我们能够确定这个重要的宿主-微生物模型系统历史上关键事件的日期。
Wolbachia are maternally inherited symbiotic bacteria, commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. The evolutionary history of endosymbionts like Wolbachia can be revealed by integrating information on infection status in natural populations with patterns of sequence variation in Wolbachia and host mitochondrial genomes. Here we use whole-genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe, and Africa to predict Wolbachia infection status, estimate relative cytoplasmic genome copy number, and reconstruct Wolbachia and mitochondrial genome sequences. Overall, 63% of Drosophila strains were predicted to be infected with Wolbachia by our in silico analysis pipeline, which shows 99% concordance with infection status determined by diagnostic PCR. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent global replacement of ancestral Wolbachia and mtDNA lineages, but our data suggest that the derived wMel lineage arose several thousand years ago, not in the 20th century as previously proposed. Our data also provide evidence that this global replacement event is incomplete and is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats. This study provides a complete genomic analysis of the evolutionary mode and temporal dynamics of the D. melanogaster–Wolbachia symbiosis, as well as important resources for further analyses of the impact of Wolbachia on host biology. Host–microbe interactions play important roles in the physiology, development, and ecology of many organisms. Studying how hosts and their microbial symbionts evolve together over time is crucial for understanding the impact that microbes have on host biology. With the advent of high-throughput sequencing technologies, it is now possible to obtain complete genomic information for hosts and their associated microbes. Here we use whole-genome sequences from ∼300 strains of the fruitfly Drosophila melanogaster to reveal the evolutionary history of this model species and its intracellular bacterial symbiont Wolbachia. The major findings of this study are that Wolbachia in D. melanogaster is inherited strictly through the egg with no evidence of horizontal transfer from other species, that the genealogies of Wolbachia and mitochondrial genomes are virtually the same, and that both Wolbachia and mitochondrial genomes show evidence for a recent incomplete global replacement event, which has left remnant lineages in North America, Europe, and Africa. We also use the fact that Wolbachia and mitochondrial genomes have the same genealogy to estimate the rate of molecular evolution for Wolbachia, which allows us to put dates on key events in the history of this important host–microbe model system.
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DOI：
10.1016/j.cub.2011.05.058
发表时间：
2011-08-09
期刊：
Current biology : CB
影响因子：
--
作者：
Edwards CJ;Suchard MA;Lemey P;Welch JJ;Barnes I;Fulton TL;Barnett R;O'Connell TC;Coxon P;Monaghan N;Valdiosera CE;Lorenzen ED;Willerslev E;Baryshnikov GF;Rambaut A;Thomas MG;Bradley DG;Shapiro B
通讯作者：
Shapiro B
影响因子：
1.9
作者：
HOFFMANN, AA
通讯作者：
HOFFMANN, AA
影响因子：
3.4
作者：
Charlat S;Duplouy A;Hornett EA;Dyson EA;Davies N;Roderick GK;Wedell N;Hurst GD
通讯作者：
Hurst GD
影响因子：
4.9
作者：
Baldo, Laura;Ayoub, Nadia A.;Werren, John H.
通讯作者：
Werren, John H.
影响因子：
10.7
作者：
Drummond, Alexei J.;Suchard, Marc A.;Rambaut, Andrew
通讯作者：
Rambaut, Andrew