Genome-informed Bradyrhizobium taxonomy: where to from here?
Genome-informed Bradyrhizobium taxonomy: where to from here?
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DOI：
10.1016/j.syapm.2019.03.006
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发表时间：
2019-07-01
影响因子：
3.4
通讯作者：
Steenkamp, Emma T.
中科院分区：
文献类型：
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作者：
Avontuur, Juanita R.;Palmer, Marike;Steenkamp, Emma T.
慢生根瘤菌被认为是最大和最多样化的根瘤菌属，但这并没有反映在描述的物种数量。虽然它是最早被确认的根瘤菌属之一，但它的分类仍然很复杂。各种当代研究表明，基因组序列信息可以简化分类决策。因此，慢生根瘤菌基因组的不断增加可能有助于新物种的描述和表征。在这项研究中，我们解决了两个目标：第一，我们回顾了可利用的基因组资源的质量和可用性慢生根瘤菌。这是通过比较基因组序列的测序技术和估计的完整性水平，包括在基因组为基础的系统发育分析。其次，我们利用这些基因组研究了慢生根瘤菌的分类地位，鉴于其多样的生活方式。虽然基因组序列的质量和完整性不同，我们的数据表明，这些基因组序列的使用是足够的分类目的。通过使用这些资源，我们推断出一个完全解决的，得到充分支持的遗传学。它将慢生根瘤菌分为七个谱系，其中三个对应于该属已知的所谓超类群。光合作用、固氮作用和光合作用等关键生活方式性状的广泛分布揭示了这些性状具有复杂的进化历史。我们提出了第一个强大的慢生根瘤菌物种的基因组序列信息的基础上，调查这一重要的细菌组合的进化。此外，这项研究提供了基础，利用基因组序列信息作为一种资源，使重要的分类决策，特别是在种和属的水平。(C)2019 Elsevier GmbH. All rights reserved.
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels. (C) 2019 Elsevier GmbH. All rights reserved.