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Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae

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Abstract

Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022T using single molecule real-time sequencing technology (SMRT) and performed comparative genomics and phylogenomics analyses. The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 tRNA genes, and 21 rRNA genes. The C. marina JCM 21022T genome contained a set of crucial genes involved in surface colonization processes. The comparative genome analysis indicated the significant differences between C. marina JCM 21022T and Cobetia amphilecti KMM 296 (formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these differences, pan and core genome analysis showed similar gene functions between the two strains. The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.

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Author notes

  1. TANG Xianghai and XU Kuipeng contributed equally to this work.

Authors and Affiliations

  1. Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China

    Xianghai Tang  (唐祥海), Kuipeng Xu  (徐奎鹏), Xiaojuan Han  (韩晓娟) & Yunxiang Mao  (茅云翔)

  2. Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

    Zhaolan Mo  (莫照兰)

  3. CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China

    Xiaojuan Han  (韩晓娟)

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  1. Xianghai Tang  (唐祥海)
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  2. Kuipeng Xu  (徐奎鹏)
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Correspondence to Yunxiang Mao  (茅云翔).

Additional information

Supported by the National Natural Science Foundation of China (Nos. 41006082, 31372517)

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Tang, X., Xu, K., Han, X. et al. Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae. J. Ocean. Limnol. 36, 528–536 (2018). https://doi.org/10.1007/s00343-017-6239-6

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  • DOI: https://doi.org/10.1007/s00343-017-6239-6

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