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Cite this paper: |
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TANG Xianghai, XU Kuipeng, HAN Xiaojuan, MO Zhaolan, MAO Yunxiang. Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae[J]. Journal of Oceanology and Limnology, 2018, 36(2): 528-536 |
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Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae |
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| TANG Xianghai1, XU Kuipeng1, HAN Xiaojuan1,3, MO Zhaolan2, MAO Yunxiang1 |
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1 Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
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;
3 CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China |
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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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| Key words:
Cobetia marina JCM 21022T|Halomonadaceae|complete genome sequence|comparative genomics|phylogenomics|surface colonization|single molecule real-time sequencing technology (SMRT)
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| Received: 2016-09-04 Revised: |
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