Department of Biological Sciences, Vanderbilt University, USA.
Genome Biol Evol. 2011;3:209-18. doi: 10.1093/gbe/evr007. Epub 2011 Feb 2.
Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studies suggest intracellular coinfections in the same host can facilitate exchange of mobile elements between obligate intracellular bacteria-a means by which these bacteria can partially mitigate the reductive forces of the intracellular lifestyle. To test whether bacteriophages transfer as single genes or larger regions between coinfections, we sequenced the genome of the obligate intracellular Wolbachia strain wVitB from the parasitic wasp Nasonia vitripennis and compared it against the prophage sequences of the divergent wVitA coinfection. We applied, for the first time, a targeted sequence capture array to specifically trap the symbiont's DNA from a heterogeneous mixture of eukaryotic, bacterial, and viral DNA. The tiled array successfully captured the genome with 98.3% efficiency. Examination of the genome sequence revealed the largest transfer of bacteriophage and flanking genes (52.2 kb) to date between two obligate intracellular coinfections. The mobile element transfer occurred in the recent evolutionary past based on the 99.9% average nucleotide identity of the phage sequences between the two strains. In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that "targeted genome capture" can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes.
噬菌体通量可以导致自由生活细菌的大部分遗传多样性。这一细菌基因组进化的原则通常不适用于专性细胞内细菌，因为它们与其他微生物的接触减少，并且基因缺失超过基因转移。然而，最近的研究表明，同一宿主内的细胞内共感染可以促进专性细胞内细菌之间的移动元件交换——这是这些细菌部分缓解细胞内生活方式的还原力的一种方式。为了测试噬菌体是否作为单个基因或更大的区域在共感染之间转移，我们对寄生黄蜂 Nasonia vitripennis 中的专性细胞内沃尔巴克氏体菌株 wVitB 的基因组进行了测序，并将其与不同的 wVitA 共感染的前噬菌体序列进行了比较。我们首次应用靶向序列捕获阵列，专门从真核生物、细菌和病毒 DNA 的异质混合物中捕获共生体的 DNA。平铺阵列成功捕获了 98.3%效率的基因组。对基因组序列的检查显示，在两个专性细胞内共感染之间，噬菌体和侧翼基因（52.2 kb）的转移是迄今为止最大的。基于两个菌株之间噬菌体序列的 99.9%平均核苷酸同一性，这种移动元件转移发生在最近的进化过程中。除了发现两种共感染的专性细胞内细菌之间发生了最近进化的和大规模的水平噬菌体转移外，我们还证明了“靶向基因组捕获”可以富集目标 DNA，从而缓解从真核生物内部的生物体聚集体中分离难以培养或纯化的共生微生物的问题。
