Garrido-Sanz Daniel, Redondo-Nieto Miguel, Martín Marta, Rivilla Rafael
Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain.
Microorganisms. 2020 May 21;8(5):774. doi: 10.3390/microorganisms8050774.
The genus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the diversity. Phylogenomic analysis of 327 genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new strains are sequenced. The genus possesses a small "hard" core genome consisting of 381 orthologous groups (OGs), while a "soft" core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the strains, while the "open" pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.
由于其巨大的代谢多样性，包括芳香族和脂肪族化合物的生物转化，该属在生物修复应用方面具有巨大潜力。对该属的比较基因组研究仅限于少数基因组，而迄今为止大量已测序菌株可以提供更多关于该属多样性的信息。对327个基因组进行系统发育基因组分析并对基因组间距离进行聚类，确定了42个系统发育基因组组和83个物种水平的聚类。稀疏模型表明，随着新菌株的测序，这些数量可能会增加。该属拥有一个由381个直系同源组（OGs）组成的小“硬”核心基因组，而当基因组覆盖率达到99.16%时，可得到一个由1253个OGs组成的“软”核心基因组。依次随机添加基因组的模型表明，少数基因组足以解释大多数菌株的共享多样性，而“开放”的泛基因组和菌株特异性基因组表明，随着新基因组仍在向整个基因组集添加更多OGs，该属的多样性将会增加。大多数红球菌拥有参与脂肪族和芳香族化合物降解的基因，而短链烷烃降解仅限于一定数量的组，其中特定的颗粒甲烷单加氧酶（pMMO）仅在WAY2菌株中发现。对红球菌基因组中的 Rieske 2Fe-2S双加氧酶的分析表明，这些酶中的大多数仍未被表征。
