Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy.
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA, USA.
Sci Rep. 2016 Jun 22;6:28428. doi: 10.1038/srep28428.
In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.
在代表地球上最大生物群落的海底深海生态系统中，病毒具有公认的关键生态作用，但它们的多样性在很大程度上仍然未知。确定病毒的分类组成对于了解病毒-宿主相互作用、它们在食物网功能和进化过程中的作用至关重要。在这里，我们比较了各种生物信息学工具（BLAST、MG-RAST、NBC、VMGAP、MetaVir、VIROME）在分析模拟病毒组和来自不同海底深海生态系统的病毒宏基因组中的病毒分类组成的性能。模拟病毒组的分析表明，所有 BLAST 工具，其次是 MetaVir 和 VMGAP，在病毒序列和菌株的归属方面更可靠。在分析环境病毒组时，tBLASTx、MetaVir、VMGAP 和 VIROME 显示出相似的序列注释效率；然而，MetaVir 和 tBLASTx 鉴定出更多的病毒株。后两种工具还鉴定出了比其他工具更广泛的病毒家族，从而更全面地了解海底深海生态系统中病毒的分类多样性。我们的研究结果强调了现有的生物信息学工具在研究海底生态系统中病毒的分类多样性方面的优势和劣势，以提高我们对海洋中病毒多样性及其与宿主多样性和生态系统功能关系的理解。
