Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate co-evolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 gigabases, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene familie, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 megabases but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host-symbiont genomes show not only tight metabolic complementarity, but also distinct signatures of co-evolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.

中文翻译：

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在深海化学共生蛤中整合宿主-内共生体基因组。

内源性与化学合成细菌的共生使许多深海无脊椎动物在热液喷口和冷渗流中壮成长，但以前有关这种共存关系的大多数研究仅集中于细菌。囊壁蛤在基于全球深海化学合成的生态系统中占主导地位。它们与大多数深海共生动物不同，它们将共生体从亲代传递给后代，从而使宿主与共生体之间能够复杂地共同进化。在这里，我们对蛤Archive Archivesica marissinica的基因组进行了测序（双壳纲：Vesicomyidae）及其细菌共生体，以了解这种共生背后的基因组/代谢整合。在1.52 gigabases处，蛤基因组编码从细菌水平转移的28个基因，大量假基因和转座因子，它们的大量扩增与带有共生体的囊泡的上升和随后的发散时间相对应。基因组在细胞过程中表现出基因家族扩展，这可能促进化学自养，包括支持能量和碳生产的气体输送，与共生体的代谢物交换以及对细菌细胞群的调节。纤维素酶基因的收缩很可能适应从浮游植物衍生到细菌性食品的转变。它还显示了细菌识别基因家族的收缩，指示对内共生体的免疫反应被抑制。内生共生芽孢杆菌的基因组减少了1.03兆碱基，但保留了硫氧化，碳固定和20种常见氨基酸的生物合成的完整途径，表明宿主高度依赖共生素进行营养。总体而言，宿主共生体基因组不仅显示出紧密的代谢互补性，而且还表现出共同进化的独特特征，使囊泡在基于化学合成的生态系统中ecosystem壮成长。