Comparative population genomics of Pacific deep-sea tubeworms and their bacterial endosymbionts: cryptic diversity and host-symbiont specificity

Vstientiferan管虫是世界各地喷口和渗漏生境中的优势类群。由于成年后缺乏消化系统，它们在营养上依赖于从当地环境中获得的硫氧化细菌内共生体。虽然水平传播应该允许吸收各种共生微生物，但传统的16S rRNA序列分析表明，每个管虫只有一个细菌系统型的克隆种群。同样的研究表明，来自同一地点的不同寄主类群可以被相同的共生系统型感染，这表明特定的共生体和寄主物种之间没有排他性的关联(专一性)。然而，来自多基因分析的多重感染和亚型变异的证据最近挑战了管虫内共生体遗传同质性的发现，这意味着到目前为止，它们的多样性在很大程度上被低估了。如果这些假设成立，那么寄主-共生体的特异性模式很可能也被忽视了，因为所研究的标记基因的变异性有限，而且关于双方的遗传变异的信息不足。我的假设是：(1)管虫是由不同细菌类型的混合物感染的，(2)宿主和共生体在物种和基因水平上都是彼此特有的。为了验证这些假说，我提议分析东太平洋冷渗漏系统中共同出现的管虫物种LamelLibrachia Barhami和Escapia spicata在地理上分布广泛的种群中的共生关系。通过将高通量限制性位点相关DNA测序与元基因组学相结合，我将在寄主和共生体中鉴定单核苷酸多态(SNP)，以获得对双方基因组多样性和种群结构的估计。然后，来自不同SNP亚群的基因数据将被用于多变量和相关统计，以确定宿主-共生体的专一性程度。我希望我的研究将促进我们对深海动物和细菌共生的理解，并为未来研究宿主-共生体相互作用如何影响双方的生态适应、遗传种群分化和进化多样化提供基础。

Vestimentiferan tubeworms are dominant taxa in vent and seep habitats worldwide. Lacking a digestive system as adults, they are nutritionally dependent on their sulfur-oxidizing bacterial endosymbionts, which are acquired from the local environment. Although horizontal transmission should allow uptake of various symbiotic microbes, traditional 16S rRNA sequence analyses suggest that every tubeworm harbors a clonal population of only one bacterial phylotype. The same studies have shown that different host taxa from the same location can be infected by the same symbiotic phylotype, indicating that there is no exclusive association (specificity) between a particular symbiont and a host species. However, evidence for multiple infections and subtype variation from multi-gene analyses has recently challenged the finding of genetic homogeneity in the tubeworm endosymbionts, implying that their diversity has so far been largely underestimated. Should these assumptions hold true, it is likely that also patterns of host-symbiont specificity have been overlooked due to limited variability of the investigated marker genes and insufficient information on the genetic variation in both partners. My hypotheses are that (1) tubeworms are infected by a heterogeneous mixture of bacterial types and that (2) hosts and symbionts are specific to each other, both at the species and genotype level. To test these hypotheses, I propose to analyze symbiotic associations in geographically widespread populations of the tubeworm species Lamellibrachia barhami and Escarpia spicata, which co-occur at cold seep systems in the eastern Pacific Ocean. By combining high-throughput restriction-site associated DNA sequencing with metagenomics, I will identify single-nucleotide polymorphisms (SNP) in hosts and symbionts to get an estimate of the genomic diversity and population structure in both partners. The genotypic data from different SNP subsets will then be used in multivariate and correlative statistics to determine the degree of host-symbiont specificity. I expect that my study will advance our understanding of symbioses between animals and bacteria in the deep sea and provide a basis for future research on how host-symbiont interactions influence ecological adaptation, genetic population differentiation and evolutionary diversification of both partners.