title: Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments.
abstract: Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Chongping
authors.initials: C
authors.lastname: Li
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Qiliang
authors.initials: Q
authors.lastname: Lai
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Guizhen
authors.initials: G
authors.lastname: Li
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Fengqin
authors.initials: F
authors.lastname: Sun
authors.affiliation: State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Marine Biological Resources, Xiamen, China; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.
authors.forename: Zongze
authors.initials: Z
authors.lastname: Shao
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D020043:Genes, Essential; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009792:Oceans and Seas; D010802:Phylogeny; D058974:Phylogeography; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S