Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives

Photosynthesis Research

Volumn 122, Issue 2, 2014, Pages 171-185

  Howard Azzeh, Mohammad ^a   Shamseer, Larissa ^a   Schellhorn, Herb E ^a   Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Akinete forming cyanobacteria; Comparative genomics; Heterocyst forming cyanobacteria; Molecular phylogeny; Molecular signatures; Nostocales

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; CLASSIFICATION; CYANOBACTERIUM; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSERVED SEQUENCE; CYANOBACTERIA; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84926099013     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11120-014-0020-x     Document Type: Article

References (64)

1. Adeolu M, Gupta RS (2013) Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Antonie Van Leeuwenhoek 104:1-24
2. Baldauf SL, Palmer JD (1993) Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90:11558-11562
3. Bhandari V, Gupta RS (2014) Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov.; Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie Van Leeuwenhoek 105:143-168
4. Castenholz RW (2001) Phylum BX cyanobacteria oxygenic photosynthetic bacteria. In Bergey's manual of systematic bacteriology. Springer, New York, pp 474-487
5. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552
6. Cavalier-Smith T (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7-76
7. Ciccarelli FD, Doerks T, Von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287
8. De Vos P, Truper HG (2000) Judicial Commission of the International Committee on Systematic Bacteriology; IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Int J Syst Evol Microbiol 50:2239-2244
9. Delwiche CF, Kuhsel M, Palmer JD (1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogenet Evol 4:110-128
10. Desikachary TV (1959) Cyanophyta, Indian Council of Agricultural Research, monographs on Algae. New Delhi, India
11. Fang G, Rocha E, Danchin A (2005) How essential are nonessential genes? Mol Biol Evol 22:2147-2156
12. Gao B, Mohan R, Gupta RS (2009) Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Microbiol 59:234-247
13. Geitler L (1932) Cyanophycea. Rabenhorst's Kryptogamen-Flora von Deutschland, Österreich und der Schweiz, Reprint 1985:14
14. Giovannoni SJ, Turner S, Olsen GJ, Barns S, Lane DJ, Pace NR (1988) Evolutionary relationships among cyanobacteria and green chloroplasts. J Bacteriol 170:3584-3592
15. Gugger MF, Hoffmann L (2004) Polyphyly of true branching cyanobacteria (Stigonematales). Int J Syst Evol Microbiol 54:349-357
16. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62:1435-1491
17. Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367-402
18. Gupta RS (2003) Evolutionary relationships among photosynthetic bacteria. Photosynth Res 76:173-183
19. Gupta RS (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 59:2510-2526
20. Gupta RS (2010) Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups. Photosynth Res 104:357-372
21. Gupta RS (2013) Molecular markers for photosynthetic bacteria and insights into the origin and spread of photosynthesis. Adv Bot Res 66:37-66
22. Gupta RS, Lali R (2013) Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov.; containing the family Desulfurobacteriaceae. Antonie Van Leeuwenhoek 104:349-368
23. Gupta RS, Mathews DW (2010) Signature proteins for the major clades of Cyanobacteria. BMC Evol Biol 10:24
24. Gupta RS, Pereira M, Chandrasekera C, Johari V (2003) Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. Int J Syst Evol Microbiol 53:1833-1842
25. Gupta RS, Chander P, George S (2013) Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov.; consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov.; and the suborder Roseiflexineae subord. nov.; containing the family Roseiflexaceae fam. nov. Antonie Van Leeuwenhoek 103:99-119
26. Harris JK, Kelley ST, Spiegelman GB, Pace NR (2003) The genetic core of the universal ancestor. Genome Res 13:407-412
27. Henson BJ, Watson LE, Barnum SR (2002) Molecular differentiation of the heterocystous cyanobacteria, Nostoc and Anabaena, based on complete NifD sequences. Curr Microbiol 45:161-164
28. Henson BJ, Hesselbrock SM, Watson LE, Barnum SR (2004) Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD. Int J Syst Evol Microbiol 54:493-497
29. Hoffmann L (2005) Nomenclature of Cyanophyta/Cyanobacteria: roundtable on the unification of the nomenclature under the Botanical and Bacteriological Codes. Algol Stud 117:13-29
30. Hoffmann L, Komarek J, Kastovsky J (2005) System of cyanoprokaryotes (cyanobacteria) state in 2004. Algol Stud 117:95-115
31. Honda D, Yokota A, Sugiyama J (1999) Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J Mol Evol 48:723-739
32. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comp Appl Biosci CABIOS 8:275-282
33. Komárek J (2002) Problems in cyanobacterial taxonomy: implication for most common toxin producing species. Rapporti Istisan 9:6-43
34. Labeda DP (2000) International committee on systematic bacteriology; IXth international (IUMS) congress of bacteriology and applied microbiology. Int J Syst Evol Microbiol 50:2245-2247
35. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948
36. Naushad HS, Lee B, Gupta RS (2014) Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Microbiol 64:366-383
37. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, USA
38. Oren A (2004) A proposal for further integration of the cyanobacteria under the Bacteriological Code. Int J Syst Evol Microbiol 54:1895-1902
39. Oren A, Garrity GM (2014) Proposal to change general consideration 5 and principle 2 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 64:309-310
40. Oren A, Komarek J, Hoffmann L (2009) Nomenclature of the Cyanophyta/Cyanobacteria/Cyanoprokaryotes: What has happened since IAC Luxembourg? Algol Stud 130:17-26
41. Parte AC (2014) LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613-D616
42. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590-D596
43. Rajaniemi P, Hrouzek P, Kastovska K, Willame R, Rantala A, Hoffmann L, Komarek J, Sivonen K (2005) Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria). Int J Syst Evol Microbiol 55:11-26
44. Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY (1979) Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J Gen Microbiol 111:1-61
45. Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454-459
46. Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804
47. Saatcioglu FAHR, Perry DJ, Pasco DS, Fagan JB (1990) Multiple DNA-binding factors interact with overlapping specificities at the aryl hydrocarbon response element of the cytochrome P450IA1 gene. Mol Cell Biol 10:6408-6416
48. Sanchez-Baracaldo P, Hayes PK, Blank CE (2005) Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. Geobiology 3:145-165
49. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S (2010) Database resources of the national center for biotechnology information. Nucleic Acids Res 38:D5-D16
50. Schoeffler AJ, May AP, Berger JM (2010) A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res 38:7830-7844
51. Shi T, Falkowski PG (2008) Genome evolution in cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci 105:2510-2515
52. Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, de Marsac NT, Rippka R (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci 110:1053-1058
53. Singh B, Gupta RS (2009) Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 281:361-373
54. Singh P, Singh SS, Elster J, Mishra AK (2013) Molecular phylogeny, population genetics, and evolution of heterocystous cyanobacteria using nifH gene sequences. Protoplasma 250:751-764
55. Stanier RY, Sistrom WR, Hansen TA, Whitton BA, Castenholz RW, Pfennig N, Gorlenko VN, Kondratieva EN, Eimhjellen KE, Whittenbury R (1978) Proposal to place the nomenclature of the cyanobacteria (blue-green algae) under the rules of the International Code of Nomenclature of Bacteria. Int J Syst Bacteriol 28:335-336
56. Swingley WD, Blankenship RE, Raymond J (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol 25:643-654
57. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
58. Turner SE, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis 1. J Eukaryot Microbiol 46:327-338
59. Wilmotte A, Herdman M (2001) Phylogenetic relationships among the cyanobacteria based on 16S rRNA sequences. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology. Springer, New York, pp 487-493
60. Woese CR (1992) Prokaryote systematics: the evolution of a science. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes. Springer, New York, pp 3-18
61. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056-1060
62. Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glockner FO, Rossello-Mora R (2010) Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291-299
63. Zehr JP, Mellon MT, Hiorns WD (1997) Phylogeny of cyanobacterial nifH genes: evolutionary implications and potential applications to natural assemblages. Microbiology 143:1443-1450
64. Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099-1108