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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

Genomic-based taxonomic classification of the family Open Access

Abstract

The family , belonging to the order , class , is globally distributed in various environments. Currently, this family consist of seven genera: , , , , , and . As more species are identified, the taxonomic status of the family should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names , , , , , , , , , and are proposed. We reclassified all species of and as species of . This study is the first genomic-based study of the family , and will contribute to further insights into the evolution of this family.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AAI , Erythrobacteraceae , evolutionary distance and phylogenomic reconstruction
Funding
This study was supported by the:
  • the National Program for Support of Top-Notch Young Professionals
    • Principle Award Recipient: Lin Xu
  • Natural Science Foundation of Zhejiang Province (Award LR17D060001)
    • Principle Award Recipient: Lin Xu
  • National Natural Science Foundation of China (Award 31770004 and 91851114)
    • Principle Award Recipient: Xue-Wei Xu
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-07-29
2024-04-29
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References

  1. Tonon LAC, Moreira APB, Thompson F et al. The family Erythrobacteraceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Heidelberg: Springer; 2014 pp 213–235
     [Google Scholar]
  2. Feng X-M, Mo Y-X, Han L, Nogi Y, Zhu Y-H et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015; 65:3658–3665 [View Article]
     [Google Scholar]
  3. Yoon J-H, Oh T-K, Park Y-H. Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:71–75 [View Article]
     [Google Scholar]
  4. Xu X-W, Wu Y-H, Wang C-S, Wang X-G, Oren A et al. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae . Int J Syst Evol Microbiol 2009; 59:2247–2253 [View Article][PubMed]
     [Google Scholar]
  5. Wu Y-H, Li G-Y, Jian S-L, Cheng H, Huo Y-Y et al. Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments. Int J Syst Evol Microbiol 2016; 66:4506–4511 [View Article][PubMed]
     [Google Scholar]
  6. Liao H, Li Y, Zhang M, Lin X, Lai Q et al. Altererythrobacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2017; 67:4851–4856 [View Article]
     [Google Scholar]
  7. Ma H, Ren H, Huang L, Luo Y. Altererythrobacter flavus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2018; 68:2265–2270 [View Article]
     [Google Scholar]
  8. Wu Y-H, Xu L, Meng F-X, Zhang D-S, Wang C-S et al. Altererythrobacter atlanticus sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:116–121 [View Article][PubMed]
     [Google Scholar]
  9. Fang C, Wu Y-H, Sun C, Wang H, Cheng H et al. Erythrobacter zhengii sp. nov., a bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2019; 69:241–248 [View Article]
     [Google Scholar]
  10. Qu J-H, Ma W-W, Li H-F, Wang X-F, Lu B-B et al. Altererythrobacter amylolyticus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1231–1236 [View Article][PubMed]
     [Google Scholar]
  11. Dahal RH, Kim J. Altererythrobacter fulvus sp. nov., a novel alkalitolerant alphaproteobacterium isolated from forest soil. Int J Syst Evol Microbiol 2018; 68:1502–1508 [View Article]
     [Google Scholar]
  12. Yuan N, Zeng Y, Feng H, Yu Z, Huang Y. Altererythrobacter xixiisoli sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2017; 67:3655–3659 [View Article]
     [Google Scholar]
  13. Subhash Y, Tushar L, Sasikala C, Ramana CV. Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int J Syst Evol Microbiol 2013; 63:4524–4532 [View Article]
     [Google Scholar]
  14. Zhao Q, Li H-R, Han Q-Q, He A-L, Nie C-Y et al. Altererythrobacter soli sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 2017; 67:454–459 [View Article]
     [Google Scholar]
  15. Xue X, Zhang K, Cai F, Dai J, Wang Y et al. Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2012; 62:28–32 [View Article]
     [Google Scholar]
  16. Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM et al. Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter . PeerJ 2015; 3:e1400 [View Article]
     [Google Scholar]
  17. Meng F-X, Li G, Fang C, Wu Y-H, Cheng H et al. Altererythrobacter aerophilus sp. nov., isolated from deep-sea water of the north-west Pacific. Int J Syst Evol Microbiol 2019; 69:1689–1695 [View Article]
     [Google Scholar]
  18. Lei X, Li Y, Chen Z, Zheng W, Lai Q et al. Altererythrobacter xiamenensis sp. nov., an algicidal bacterium isolated from red tide seawater. Int J Syst Evol Microbiol 2014; 64:631–637 [View Article]
     [Google Scholar]
  19. Li D-D, Zhang Y-Q, Peng M, Wang N, Wang X-J et al. Erythrobacter xanthus sp. nov., isolated from surface seawater of the South China Sea. Int J Syst Evol Microbiol 2017; 67:2459–2464 [View Article][PubMed]
     [Google Scholar]
  20. Park S, Jung Y-T, Park J-M, Yoon J-H. Altererythrobacter confluentis sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2016; 66:4002–4008 [View Article]
     [Google Scholar]
  21. Jung Y-T, Park S, Lee J-S, Yoon J-H. Altererythrobacter aquiaggeris sp. nov., isolated from water of an estuary bank. Int J Syst Evol Microbiol 2017; 67:3410–3416 [View Article]
     [Google Scholar]
  22. Park S, Won SM, Yoon J-H. Erythrobacter marisflavi sp. nov., isolated from isolated from estuary water. Int J Syst Evol Microbiol 2019; 69:2696–2702 [View Article]
     [Google Scholar]
  23. Fuerst JA, Hawkins JA, Holmes A, Sly LI, Moore CJ et al. Porphyrobacter neustonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-synthesizing budding bacterium from fresh water. Int J Syst Bacteriol 1993; 43:125–134 [View Article]
     [Google Scholar]
  24. Furuhata K, Edagawa A, Miyamoto H, Kawakami Y, Fukuyama M. Porphyrobacter colymbi sp. nov. isolated from swimming pool water in Tokyo, Japan. J Gen Appl Microbiol 2013; 59:245–250 [View Article]
     [Google Scholar]
  25. Yuan C-G, Chen X, Jiang Z, Chen W, Liu L et al. Altererythrobacter lauratis sp. nov. and Altererythrobacter palmitatis sp. nov., isolated from a Tibetan hot spring. Antonie van Leeuwenhoek 2017; 110:1077–1086 [View Article]
     [Google Scholar]
  26. Rainey FA, Silva J, Nobre MF, Silva MT, da Costa MS. Porphyrobacter cryptus sp. nov., a novel slightly thermophilic, aerobic, bacteriochlorophyll a-containing species. Int J Syst Evol Microbiol 2003; 53:35–41 [View Article]
     [Google Scholar]
  27. Hanada S, Kawase Y, Hiraishi A, Takaichi S, Matsuura K et al. Porphyrobacter tepidarius sp. nov., a moderately thermophilic aerobic photosynthetic bacterium isolated from a hot spring. Int J Syst Bacteriol 1997; 47:408–413 [View Article]
     [Google Scholar]
  28. Xue H, Piao C-G, Guo M-W, Wang L-F, Fang W et al. Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2016; 66:4543–4548 [View Article]
     [Google Scholar]
  29. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a . Int J Syst Bacteriol 1982; 32:211–217 [View Article]
     [Google Scholar]
  30. Liu Y-H, Fang B-Z, Dong Z-Y, Li L, Mohamad OAA et al. Croceibacterium gen. nov., with description of Croceibacterium ferulae sp. nov., an endophytic bacterium isolated from Ferula sinkiangensis K. M. Shen and reclassification of Porphyrobacter mercurialis as Croceibacterium mercuriale comb. nov. Int J Syst Evol Microbiol 2019; 69:2547–2554 [View Article]
     [Google Scholar]
  31. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994; 44:427–434 [View Article]
     [Google Scholar]
  32. Fidalgo C, Rocha J, Martins R, Proença DN, Morais PV et al. Altererythrobacter halimionae sp. nov. and Altererythrobacter endophyticus sp. nov., two endophytes from the salt marsh plant Halimione portulacoides . Int J Syst Evol Microbiol 2017; 67:3057–3062 [View Article]
     [Google Scholar]
  33. Kumar NR, Nair S, Langer S, Busse H-J, Kämpfer P. Altererythrobacter indicus sp. nov., isolated from wild rice (Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 2008; 58:839–844 [View Article]
     [Google Scholar]
  34. Nedashkovskaya OI, Cho S-H, Joung Y, Joh K, Kim MN et al. Altererythrobacter troitsensis sp. nov., isolated from the sea urchin Strongylocentrotus intermedius . Int J Syst Evol Microbiol 2013; 63:93–97 [View Article]
     [Google Scholar]
  35. Zhuang L, Lin B, Xu L, Li G, Wu C-J et al. Erythrobacter spongiae sp. nov., isolated from marine sponge. Int J Syst Evol Microbiol 2019; 69:1111–1116 [View Article][PubMed]
     [Google Scholar]
  36. Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM et al. Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. Syst Appl Microbiol 2005; 28:123–130 [View Article]
     [Google Scholar]
  37. Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T et al. The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005; 55:1907–1919 [View Article]
     [Google Scholar]
  38. Kwon KK, Woo J-H, Yang S-H, Kang J-H, Kang SG et al. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol 2007; 57:2207–2211 [View Article]
     [Google Scholar]
  39. Parte AC. LPSN – list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
     [Google Scholar]
  40. Park S, Park J-M, Yoon J-H. Altererythrobacter aquimixticola sp. nov., isolated from sediment sampled at the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2019; 69:2408–2414 [View Article]
     [Google Scholar]
  41. Park S, Park J-M, Oh T-K, Yoon J-H. Altererythrobacter insulae sp. nov., a lipolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1009–1015 [View Article]
     [Google Scholar]
  42. Lee SD. Altererythrobacter lutipelagi sp. nov., isolated from a tidal mudflat, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2019; 69:1980–1985 [View Article]
     [Google Scholar]
  43. Kang H, Kim H, Joh K. Altererythrobacter maritimus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2019; 69:1566–1572 [View Article]
     [Google Scholar]
  44. Kristyanto S, Lee SD, Kim J. Porphyrobacter algicida sp. nov., an algalytic bacterium isolated from seawater. Int J Syst Evol Microbiol 2017; 67:4526–4533 [View Article]
     [Google Scholar]
  45. Jiao N, Zhang Y, Zeng Y, Hong N, Liu R et al. Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ Microbiol 2007; 9:3091–3099 [View Article]
     [Google Scholar]
  46. Zheng Q, Lin W, Liu Y, Chen C, Jiao N. A comparison of 14 Erythrobacter genomes provides insights into the genomic divergence and scattered distribution of phototrophs. Front Microbiol 2016; 7:984 [View Article]
     [Google Scholar]
  47. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM et al. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 2002; 415:630–633 [View Article]
     [Google Scholar]
  48. Li Z-Y, Wu Y-H, Huo Y-Y, Cheng H, Wang C-S et al. Complete genome sequence of a benzo[a]pyrene-degrading bacterium Altererythrobacter epoxidivorans CGMCC 1.7731T . Mar Genomics 2016; 25:39–41 [View Article][PubMed]
     [Google Scholar]
  49. Alonso-Gutiérrez J, Figueras A, Albaigés J, Jiménez Núria, Viñas M et al. Bacterial communities from shoreline environments (Costa da Morte, northwestern Spain) affected by the Prestige oil spill. Appl Environ Microbiol 2009; 75:3407–3418 [View Article]
     [Google Scholar]
  50. Hu Y, MacMillan JB, Erythrazoles A-B. Erythrazoles A-B, cytotoxic benzothiazoles from a marine-derived Erythrobacter sp. Org Lett 2011; 13:6580–6583 [View Article][PubMed]
     [Google Scholar]
  51. Hu Y, Legako AG, Espindola APDM, MacMillan JB. Erythrolic acids A–E, meroterpenoids from a marine-derived Erythrobacter sp. J Org Chem 2012; 77:3401–3407 [View Article]
     [Google Scholar]
  52. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
     [Google Scholar]
  53. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217–222 [View Article]
     [Google Scholar]
  54. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article]
     [Google Scholar]
  55. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains bacteria and archaea. Nat Commun 2019; 10:5477 [View Article]
     [Google Scholar]
  56. de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative genomics and phylogenomic analysis of the genus Salinivibrio . Front Microbiol 2019; 10:2104 [View Article]
     [Google Scholar]
  57. Liu Y, Lai Q, Shao Z. Genome-based analysis reveals the taxonomy and diversity of the family Idiomarinaceae . Front Microbiol 2018; 9:2453 [View Article]
     [Google Scholar]
  58. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article]
     [Google Scholar]
  59. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article]
     [Google Scholar]
  60. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
     [Google Scholar]
  61. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article]
     [Google Scholar]
  62. Jung Y-T, Park S, Lee J-S, Yoon J-H. Altererythrobacter aestiaquae sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:3943–3949 [View Article]
     [Google Scholar]
  63. Park SC, Baik KS, Choe HN, Lim CH, Kim HJ et al. Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:709–715 [View Article]
     [Google Scholar]
  64. Park S, Jung Y-T, Choi SJ, Yoon J-H. Altererythrobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:3446–3451 [View Article]
     [Google Scholar]
  65. Zhang G, Yang Y, Wang L. Altererythrobacter aurantiacus sp. nov., isolated from deep-sea sediment. Antonie van Leeuwenhoek 2016; 109:1245–1251 [View Article]
     [Google Scholar]
  66. Zhang W, Yuan X, Feng Q, Zhang R, Zhao X et al. Altererythrobacter buctense sp. nov., isolated from mudstone core. Antonie van Leeuwenhoek 2016; 109:793–799 [View Article]
     [Google Scholar]
  67. Jeong SH, Jin HM, Lee HJ, Jeon CO. Altererythrobacter gangjinensis sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2013; 63:971–976 [View Article]
     [Google Scholar]
  68. Yoon J-H, Kang KH, Yeo S-H, Oh T-K. Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1167–1170 [View Article][PubMed]
     [Google Scholar]
  69. Lai Q, Yuan J, Shao Z. Altererythrobacter marinus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2009; 59:2973–2976 [View Article]
     [Google Scholar]
  70. Yang Y, Zhang G, Sun Z, Cheung MK, Huang C. Altererythrobacter oceanensis sp. nov., isolated from the Western Pacific. Antonie van Leeuwenhoek 2014; 106:1191–1198 [View Article]
     [Google Scholar]
  71. Liang X, Lin H, Wang K, Liao Y, Lai Q et al. Altererythrobacter salegens sp. nov., a slightly halophilic bacterium isolated from surface sediment. Int J Syst Evol Microbiol 2017; 67:909–913 [View Article]
     [Google Scholar]
  72. Kim J-H, Yoon J-H, Kim W. Altererythrobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:5424–5429 [View Article]
     [Google Scholar]
  73. Yoon J-H, Kang KH, Oh T-K, Park Y-H. Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004; 54:1981–1985 [View Article]
     [Google Scholar]
  74. Xing T, Liu Y, Wang N, Xu B, Liu K et al. Erythrobacter arachoides sp. nov., isolated from ice core. Int J Syst Evol Microbiol 2017; 67:4235–4239 [View Article]
     [Google Scholar]
  75. Denner EBM, Vybiral D, Koblízek M, Kämpfer P, Busse H-J et al. Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea . Int J Syst Evol Microbiol 2002; 52:1655–1661 [View Article][PubMed]
     [Google Scholar]
  76. Yoon B-J, Lee D-H, Oh D-C. Erythrobacter jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1421–1426 [View Article]
     [Google Scholar]
  77. Wu H-X, Lai PY, Lee OO, Zhou X-J, Miao L et al. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the red sea. Int J Syst Evol Microbiol 2012; 62:1348–1353 [View Article][PubMed]
     [Google Scholar]
  78. Xu L, Wu Y-H, Cheng H, Sun C, Han B-N et al. Complete genome sequence of Erythrobacter seohaensis SW-135T sheds light on the ecological role of the genus Erythrobacter for phosphorus cycle in the marine environment. Mar Genomics 2018; 40:21–24 [View Article]
     [Google Scholar]
  79. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
     [Google Scholar]
  80. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
     [Google Scholar]
  81. Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
     [Google Scholar]
  82. Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57 [View Article]
     [Google Scholar]
  83. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  84. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
     [Google Scholar]
  85. Xu L, Wu Y-H, Zhou P, Cheng H, Liu Q et al. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018; 19:385 [View Article]
     [Google Scholar]
  86. Xu L, Ye K-X, Dai W-H, Sun C, Xu L-H, K-X Y, L-H X et al. Comparative genomic insights into secondary metabolism biosynthetic gene cluster distributions of marine Streptomyces . Mar Drugs 2019; 17:498 [View Article]
     [Google Scholar]
  87. Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF et al. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article]
     [Google Scholar]
  88. Park S, Jung Y-T, Choi SJ, Yoon J-H. Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:2964–2969 [View Article]
     [Google Scholar]
  89. Xu L, Wu Y-H, Jian S-L, Wang C-S, Wu M et al. Pseudohongiella nitratireducens sp. nov., isolated from seawater, and emended description of the genus Pseudohongiella . Int J Syst Evol Microbiol 2016; 66:5155–5160 [View Article]
     [Google Scholar]
  90. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article]
     [Google Scholar]
  91. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  92. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  93. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article]
     [Google Scholar]
  94. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article]
     [Google Scholar]
  95. Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 2006; 34:W609–W612 [View Article]
     [Google Scholar]
  96. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article]
     [Google Scholar]
  97. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
     [Google Scholar]
  98. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  99. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
     [Google Scholar]
  100. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  101. Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graph Stat 1996; 5:299–314
     [Google Scholar]
  102. Tamames J. Evolution of gene order conservation in prokaryotes. Genome Biol 2001; 2:research0020 [View Article][PubMed]
     [Google Scholar]
  103. Patenge N, Berendes A, Engelhardt H, Schuster SC, Oesterhelt D. The fla gene cluster is involved in the biogenesis of flagella in Halobacterium salinarum . Mol Microbiol 2001; 41:653–663 [View Article][PubMed]
     [Google Scholar]
  104. Hiraishi A, Yonemitsu Y, Matsushita M, Shin YK, Kuraishi H et al. Characterization of Porphyrobacter sanguineus sp. nov., an aerobic bacteriochlorophyll-containing bacterium capable of degrading biphenyl and dibenzofuran. Arch Microbiol 2002; 178:45–52 [View Article][PubMed]
     [Google Scholar]
  105. Yoon J-H, Lee M-H, Oh T-K. Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst Evol Microbiol 2004; 54:2231–2235 [View Article][PubMed]
     [Google Scholar]
  106. Yoon J-H, Kang S-J, Lee M-H, Oh HW, Oh T-K. Porphyrobacter dokdonensis sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2006; 56:1079–1083 [View Article][PubMed]
     [Google Scholar]
  107. Wang Q, Suzuki A, Mariconda S, Porwollik S, Harshey RM. Sensing wetness: a new role for the bacterial flagellum. EMBO J 2005; 24:2034–2042 [View Article][PubMed]
     [Google Scholar]
  108. Bardy SL, Ng SYM, Jarrell KF. Prokaryotic motility structures. Microbiology 2003; 149:295–304 [View Article][PubMed]
     [Google Scholar]
  109. Zhuang L, Liu Y, Wang L, Wang W, Shao Z. Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2015; 65:3714–3719 [View Article][PubMed]
     [Google Scholar]
  110. Huang Y, Zeng Y, Feng H, Wu Y, Xu X. Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus . Int J Syst Evol Microbiol 2015; 65:1531–1536 [View Article][PubMed]
     [Google Scholar]
  111. Fan Z-Y, Xiao Y-P, Hui W, Tian G-R, Lee J-S et al. Altererythrobacter dongtanensis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2011; 61:2035–2039 [View Article][PubMed]
     [Google Scholar]
  112. Kang JW, Kim MS, Lee JH, Baik KS, Seong CN. Altererythrobacter rigui sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 66:2491–2496 [View Article][PubMed]
     [Google Scholar]
  113. Xu M, Xin Y, Yu Y, Zhang J, Zhou Y et al. Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2010; 60:2215–2220 [View Article][PubMed]
     [Google Scholar]
  114. Jung Y-T, Park S, Lee J-S, Yoon J-H. Erythrobacter lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:4184–4190 [View Article][PubMed]
     [Google Scholar]
  115. Matsumoto M, Iwama D, Arakaki A, Tanaka A, Tanaka T et al. Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment. Int J Syst Evol Microbiol 2011; 61:2956–2961 [View Article][PubMed]
     [Google Scholar]
  116. Seo SH, Lee SD. Altererythrobacter marensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2010; 60:307–311 [View Article][PubMed]
     [Google Scholar]
  117. Lee YS, Lee D-H, Kahng H-Y, Kim EM, Jung JS. Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2010; 60:1413–1417 [View Article][PubMed]
     [Google Scholar]
  118. Lei X, Zhang H, Chen Y, Li Y, Chen Z et al. Erythrobacter luteus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2015; 65:2472–2478 [View Article][PubMed]
     [Google Scholar]
  119. Jung Y-T, Park S, Oh T-K, Yoon J-H. Erythrobacter marinus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:2050–2055 [View Article][PubMed]
     [Google Scholar]
  120. Wu Y-H, Cheng H, Zhou P, Huo Y-Y, Wang C-S et al. Complete genome sequence of the heavy metal resistant bacterium Altererythrobacter atlanticus 26DY36T, isolated from deep-sea sediment of the North Atlantic Mid-ocean ridge. Mar Genomics 2015; 24:289–292 [View Article][PubMed]
     [Google Scholar]
  121. Cheng H, Wu Y-H, Huo Y-Y, Zhou P, Liu Q et al. Complete genome sequence of Altererythrobacter dongtanensis KCTC 22672T, isolated from a tidal flat. Mar Genomics 2017; 34:11–14 [View Article]
     [Google Scholar]
  122. Shi X-L, Wu Y-H, Cheng H, Zhang X-Q, Wang C-S et al. Complete genome sequence of astaxanthin-producing bacterium Altererythrobacter ishigakiensis NBRC 107699. Mar Genomics 2016; 30:77–79 [View Article][PubMed]
     [Google Scholar]
  123. Zhou P, Wu Y-H, Cheng H, Wang C-S, Xu X-W, Y-H W, X-W X. Draft genome sequence of Altererythrobacter troitsensis JCM 17037, isolated from the sea urchin Strongylocentrotus intermedius . Genome Announc 2016; 4:e01556–15 [View Article][PubMed]
     [Google Scholar]
  124. Coil DA, Eisen JA. Draft genome sequence of Porphyrobacter mercurialis (sp. nov.) strain Coronado. Genome Announc 2015; 3:e00856–15 [View Article][PubMed]
     [Google Scholar]
  125. Wu Y-H, Cheng H, Huo Y-Y, Xu L, Liu Q et al. Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T . Stand Genomic Sci 2017; 12:88 [View Article][PubMed]
     [Google Scholar]
  126. Xu L, Wu Y-H, Zhou Y-G, Cheng H, Liu Q et al. Complete genome sequence of Erythrobacter gangjinensis CGMCC 1.15024T with two chromosomes. Mar Genomics 2017; 34:15–18 [View Article]
     [Google Scholar]
  127. Wang Y, Zhang R, Zheng Q, Jiao N. Draft genome sequences of two marine phototrophic bacteria, Erythrobacter longus strain DSM 6997 and Erythrobacter litoralis strain DSM 8509. Genome Announc 2014; 2:e00677–14 [View Article][PubMed]
     [Google Scholar]
  128. Liu Q, Wu Y-H, Cheng H, Xu L, Wang C-S et al. Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434. Stand Genomic Sci 2017; 12:32 [View Article][PubMed]
     [Google Scholar]
  129. Gao Y, Wu Y-H, Xu L, Cheng H, Wang C-S et al. Complete genome sequence of Qipengyuania sediminis CGMCC 1.12928T, shed light on its role in matter-cycle and cold adaption mechanism of the genus Qipengyuania . Curr Microbiol 2019; 76:988–994 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004293
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Genomic-based taxonomic classification of the family Erythrobacteraceae
Int J Syst Evol Microbiol 70, 4470 (2020); https://doi.org/10.1099/ijsem.0.004293
/content/journal/ijsem/10.1099/ijsem.0.004293
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