Gene duplication drives genome expansion in a major lineage of Thaumarchaeota.
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota.
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DOI：
10.1038/s41467-020-19132-x
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发表时间：
2020-10-30
影响因子：
16.6
通讯作者：
Gubry-Rangin C
中科院分区：
文献类型：
--
作者：
Sheridan PO;Raguideau S;Quince C;Holden J;Zhang L;Thames Consortium;Williams TA;Gubry-Rangin C
Thaumarchaeota门的氨氧化古菌是氮循环中的重要生物，但将其辐射到不同生态系统中的机制仍有待探索。在这里，现有的thaumarchaeotal基因组与12个基因组属于以前采样不足的亚硝化球菌目调查横向基因转移（LGT），基因复制和损失的影响thaumarchaeotal进化。我们揭示了早期LGT后基因复制在驱动基因组扩增中的重要作用。特别是，两个大的LGT事件被确定为亚硝化球菌目，这些基因家族的命运是高度谱系特异性的，在一些后代谱系中丢失，但在其他谱系中进行广泛的复制，这表明了生态位特异性的作用。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，这可能促进了土壤和沉积物中的生态位专门化。总的来说，我们的研究结果表明，LGT其次是基因复制驱动亚硝化单胞菌的进化，突出了以前低估的古细菌基因组扩增机制。古菌门的氨氧化古菌是氮循环中的重要生物。利用12个新的基因组，这项研究发现的证据表明，亚硝化球菌的进化是由横向基因转移，然后基因复制。
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. Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle. Using 12 new genomes, this study finds evidence that Nitrososphaerales evolution was marked by lateral gene transfer followed by gene duplication.
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影响因子：
4.4
作者：
Cobo-Simón M;Tamames J
通讯作者：
Tamames J
DOI：
10.1073/pnas.1109000108
发表时间：
2011-12-27
影响因子：
11.1
作者：
Gubry-Rangin, Cecile;Hai, Brigitte;Nicol, Graeme W.
通讯作者：
Nicol, Graeme W.
影响因子：
4.8
作者：
Corbin, CJ;Mapes, SM;Conley, AJ
通讯作者：
Conley, AJ
影响因子：
5.2
作者：
Daebeler A;Herbold CW;Vierheilig J;Sedlacek CJ;Pjevac P;Albertsen M;Kirkegaard RH;de la Torre JR;Daims H;Wagner M
通讯作者：
Wagner M
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T