Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
Department of Molecular Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA.
Mol Biol Evol. 2017 Nov 1;34(11):2747-2761. doi: 10.1093/molbev/msx188.
Even the simplest microbial-eukaryotic mutualisms are comprised of entire populations of symbionts at the level of the host individual. Early work suggested that these intrahost populations maintain low genetic diversity as a result of transmission bottlenecks or to avoid competition between symbiont genotypes. However, the amount of genetic diversity among symbionts within a single host remains largely unexplored. To address this, we investigated the chemosynthetic symbiosis between the bivalve Solemya velum and its intracellular bacterial symbionts, which exhibits evidence of both vertical and horizontal transmission. Intrahost symbiont populations were sequenced to high coverage (200-1,000×). Analyses of nucleotide diversity revealed that the symbiont genome sequences were largely homogeneous within individual host specimens, consistent with vertical transmission, except for particular regions that were polymorphic in ∼20% of host specimens. These variant sites were also found segregating in other host individuals from the same population, colocalized to several regions of the genome, and consistently co-occurred on the same short read pairs (derived from the same chromosome). These results strongly suggest that these variant haplotypes originated through recombination events, potentially during prior mixed infections or in the external environment, rather than as novel mutations within symbiont populations. This abundant genetic diversity could have a profound influence on symbiont evolution as it provides the opportunity for selection to limit the extent of reductive genome evolution commonly seen in obligate intracellular bacteria and to enable the evolution of adaptive genotypes.
即使是最简单的微生物-真核共生体，也是由宿主个体水平上的整个共生种群组成的。早期的研究表明，由于传播瓶颈或为避免共生体基因型之间的竞争，这些宿主内种群的遗传多样性较低。然而，单个宿主内共生体之间的遗传多样性数量在很大程度上仍未得到探索。为了解决这个问题，我们研究了双壳类软体动物 Solemya velum 与其细胞内细菌共生体之间的化学合成共生关系，该共生关系表现出垂直和水平传播的证据。对宿主内共生种群进行了高覆盖率（200-1000 倍）测序。核苷酸多样性分析表明，除了在大约 20%的宿主样本中存在多态性的特定区域外，共生体基因组序列在个体宿主样本中基本是同质的，这与垂直传播一致。这些变体位点也在同一群体的其他宿主个体中分离出来，与基因组的几个区域共定位，并且经常在相同的短读对（来自同一染色体）上共同出现。这些结果强烈表明，这些变体单倍型是通过重组事件产生的，可能是在先前的混合感染或外部环境中，而不是共生体种群中新出现的突变。这种丰富的遗传多样性可能对共生体进化产生深远影响，因为它为选择提供了机会，可以限制通常在专性细胞内细菌中看到的还原基因组进化的程度，并促进适应性基因型的进化。
