School of Biological Sciences, University of Aberdeen, Aberdeen, UK.
School of Biological Sciences, University of Bristol, Bristol, UK.
Nat Commun. 2020 Oct 30;11(1):5494. doi: 10.1038/s41467-020-19132-x.
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
氨氧化古菌门（Thaumarchaeota）是氮循环中的重要生物，但驱动它们辐射到不同生态系统的机制仍未得到充分探索。在这里，我们用 12 个属于以前采样不足的硝化螺旋菌目（Nitrososphaerales）的基因组来补充现有的氨氧化古菌基因组，以研究水平基因转移（LGT）、基因复制和丢失对氨氧化古菌进化的影响。我们揭示了基因复制在早期 LGT 之后驱动基因组扩张的主要作用。特别是，有两个大型的 LGT 事件被识别到硝化螺旋菌目，并且这些基因家族的命运在很大程度上是谱系特异性的，在一些后裔谱系中丢失，但在其他谱系中经历了广泛的复制，这表明了特定生态位的作用。值得注意的是，一些参与碳水化合物运输或辅酶代谢的基因被复制，可能有助于土壤和沉积物中的生态位特化。总的来说，我们的结果表明，LGT 随后的基因复制驱动了硝化螺旋菌目的进化，突出了古菌中基因组扩张的一个以前未被充分认识的机制。
