Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.
Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.
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DOI：
10.1093/gbe/evt036
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发表时间：
2013
影响因子：
3.3
通讯作者：
Sobral BW
中科院分区：
文献类型：
--
作者：
Driscoll T;Gillespie JJ;Nordberg EK;Azad AF;Sobral BW
真核基因组测序项目通常会产生细菌 DNA 序列，这些数据通常被视为微生物污染。然而，这些序列也可能表明共生基因或横向基因转移（LGT）到宿主基因组。这些细菌序列可以提供有关真核生物与微生物相互作用的线索。在这里，我们使用原始动物 Trichoplax adhaerens（后生动物： Placozoa）的基因组来寻找细菌 DNA 序列的存在，该动物已知含有未表征的革兰氏阴性内共生体。对从基因组组装（181 个细菌编码序列 [CDS]）和跟踪读取档案（16S rDNA）中提取的数据进行生物信息学和系统发育分析，揭示了显性变形菌谱强烈偏向于立克次氏体（Alphaproteobacteria）基因组。通过对变形菌基因组中保守的 16S rDNA 和 113 个蛋白质进行系统发育分析，以及鉴定 27 个立克次体特征基因，我们提出了 T. adhaerens 的立克次体内共生体 (RETA)。大多数（93%）已鉴定的细菌 CDS 属于含有原核样基因的小支架；然而，在由真核样基因组成的大型支架上发现了 12 个 CDS，这表明 T. adhaerens 可能最近获得了细菌基因。这些假定的 LGT 可能与长生动物的水生生态位一致，并与 RETA 共生。这项工作强调了真核基因组项目丰富且相对未开发的资源，用于保存与宿主-微生物相互作用相关的数据。未知（或特征不明确）的细菌物种的性质可能只能通过宿主基因组测序项目的分析来显现，特别是如果这些物种对细胞培养具有抗性，许多专性细胞内微生物也是如此。我们的工作为这种方法提供了方法论见解。
Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan’s aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host–microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.
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