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首页> 外文期刊>BMC Genomics >Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain
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Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain

机译：发光的Photorhabdus luminescens亚种的表型和基因组比较。 laumondii TT01和广泛使用的耐利福平的光致光菌实验室菌株

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摘要

Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has been described earlier. Subsequently, a rifampicin resistant P. luminescens strain has been generated with superior possibilities for experimental characterization. This strain, which is widely used in research, was described as a spontaneous rifampicin resistant mutant of TT01 and is known as TT01-RifR. Unexpectedly, upon phenotypic comparison between the rifampicin resistant strain and its presumed parent TT01, major differences were found with respect to bioluminescence, pigmentation, biofilm formation, haemolysis as well as growth. Therefore, we renamed the strain TT01-RifR to DJC. To unravel the genomic basis of the observed differences, we generated a complete genome sequence for strain DJC using the PacBio long read technology. As strain DJC was supposed to be a spontaneous mutant, only few sequence differences were expected. In order to distinguish these from potential sequencing errors in the published TT01 genome, we re-sequenced a derivative of strain TT01 in parallel, also using the PacBio technology. The two TT01 genomes differed at only 30 positions. In contrast, the genome of strain DJC varied extensively from TT01, showing 13,000 point mutations, 330 frameshifts, and 220 strain-specific regions with a total length of more than 300?kb in each of the compared genomes. According to the major phenotypic and genotypic differences, the rifampicin resistant P. luminescens strain, now named strain DJC, has to be considered as an independent isolate rather than a derivative of strain TT01. Strains TT01 and DJC both belong to P. luminescens subsp. laumondii.
机译：发光杆菌是一种肠细菌，它与土壤线虫相互关联，对多种昆虫具有高致病性。菌株P. luminescens亚种的完整基因组序列。 laumondii TT01最初是在特立尼达和多巴哥分离的，此前已有报道。随后，产生了具有利福平抗性的P. luminescens菌株，具有用于实验表征的绝佳可能性。该菌株在研究中被广泛使用，被描述为TT01的自发利福平抗性突变体，被称为TT01-RifR。出乎意料的是，在利福平抗性菌株与其假定的母体TT01之间的表型比较中，发现在生物发光，色素沉着，生物膜形成，溶血以及生长方面存在主要差异。因此，我们将菌株TT01-RifR重命名为DJC。为了弄清观察到的差异的基因组基础，我们使用PacBio长读技术为DJC菌株生成了完整的基因组序列。由于菌株DJC被认为是自发突变体，因此预期只有很少的序列差异。为了将这些错误与已发布的TT01基因组中的潜在测序错误区分开，我们也使用PacBio技术并行地对TT01菌株的衍生物进行了重新测序。两个TT01基因组仅在30个位置不同。相比之下，DJC菌株的基因组与TT01的变异很大，在每个比较的基因组中显示13,000个点突变，330个移码和220个菌株特异性区域，总长度超过300？kb。根据主要的表型和基因型差异，必须将耐利福平的光合疟原虫菌株（现命名为DJC菌株）视为独立的分离株，而不是菌株TT01的衍生物。菌株TT01和DJC都属于发光假单胞菌亚种。劳蒙第。

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