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Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427T (=DSM 26321T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains

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Abstract

Massilia oculi sp. nov. of type strain CCUG 43427T is a Gram-negative, rod-shaped, nonspore-forming bacterium, which was recently isolated from the eye of a patient suffering from endophthalmitis and was described as novel species in Massilia genus. In this study, we present the complete genome sequence of this strain by using Pacbio SMRT cell platform and compare this sequence with the genomes of 30 Massilia representative strains. Also, a comprehensive search was conducted for genes and proteins involved in antibiotic resistance and pathogenicity. The genome of CCUG 43427T is 5,844,653 bp with 65.55% GC content. This genome contains four prophages and four genomic islands (GIs). The cobalt/zinc/cadmium transporter locus CzcABCD is included in these GIs. This GI was predicted to play important role in bacterial heavy-metal tolerance. The in silico genome analysis also revealed that this strain contains a lot of antibiotic resistance and pathogenicity related genes. This result suggested that this strain may has evolved a wide arsenal of weapons for pathogenicity and survival. Genome comparison among CCUG 43427T and other 30 Massilia strains revealed that more than 400 genes are unique in CCUG 43427T. Among these, one gene cluster, which was annotated to be important for LOS biosynthesis, catalytic mechanism and the substrate specificity of the enzyme, was predicted to be horizontally transferred by using phylogenies and biased GC content.

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Acknowledgements

This work was supported by National Key R&D Program of China (2017YFD0201108, 2018YFD0201202), Zhejiang National Natural Science Foundation of China (LY17C010006) and State Key Laboratory for Biology of Plant Diseases and Insect Pests (SKLOF201802).

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Author notes

  1. WeiJie Song and Sai Wang have contribute equally.

Authors and Affiliations

  1. Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China

    WeiJie Song, Sai Wang & Bo Zhu

  2. College of Life Sciences, Zhejiang Sci-Tech University, Road 2, Hangzhou, 310018, Zhejiang, China

    Sai Wang

  3. Blood Transfusion Department of Zhejiang Province People’s Hospital, Hangzhou, 310014, Zhejiang, China

    Jian Shen

  4. State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China

    Bo Zhu

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  1. WeiJie Song
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Corresponding authors

Correspondence to Jian Shen or Bo Zhu.

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Fig. S1

. Circular map of the chromosome of M. oculi CCUG 43427T and other fully sequenced Massilia genomes. The tracks from the outside to inside: M. oculi CCUG 43427T, M. timonae NEU, M. timonae CCUG 45783, Massilia sp. KIM, M. niastensis DSM 21313, Massilia sp. LC238, M. alkalitolerans DSM 17462, M. yuzhufengensis, Massilia sp. BSC265, Massilia sp. WG5, Massilia sp. Root133, Massilia sp. Leaf139, Massilia sp. JS1662, Massilia sp. PDC64, Massilia sp. Root1485, Massilia sp. WF1, M. putida 6NM-7T, Massilia sp. Root335, M. phosphatilytica, Massilia sp. 9096, M. eurypsychrophila, M. namucuonensis, Massilia sp. Root418, Massilia sp. Root351, M. armeniaca ZMN-3, Massilia sp. GV045, Massilia sp. GV016, M. psychrophilum B2, M. glaciei, Massilia sp. NR 4-1, Massilia sp. CF038, GCContent and GC Skew. (JPG 4343 KB)

Fig. S2

. Rooted phylogenomic tree of M. oculi CCUG 43427T and other Massilia genomes by using single-copy-gene concatenated method. The tree shown here was calculated by Maximum Likelihood (ML) algorithm plus LG+F+R8 model. Numbers at nodes indicate percentages of occurrence in 1000 bootstrapped trees; only values greater than 50% are shown. Bar, 0.01 substitutions per site. (JPG 2913 KB)

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Song, W., Wang, S., Shen, J. et al. Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427T (=DSM 26321T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains. Curr Microbiol 76, 1082–1086 (2019). https://doi.org/10.1007/s00284-018-1597-7

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  • DOI: https://doi.org/10.1007/s00284-018-1597-7

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