Signature proteins for the major clades of Cyanobacteria.

BMC Evolutionary Biology
Radhey S Gupta, Divya W Mathews

Abstract

The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades. A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 and Prochlor. marinus subsp. marinus CCMP1375 to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most) cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i) 14 proteins for a deep branching clade (Clade A) of Gloebacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a); (ii) 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii) 60 proteins that are specific for a clade (Clade C) consisting of various marine unicellular cyanobacteria (vi...Continue Reading

References

Jun 1, 1995·Molecular Phylogenetics and Evolution·C F DelwicheJ D Palmer
Sep 1, 1994·Computer Applications in the Biosciences : CABIOS·Y Van de Peer, R De Wachter
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 12, 1998·Trends in Biochemical Sciences·F JeanmouginT J Gibson
Jun 11, 1999·Current Opinion in Structural Biology·A Danchin
Oct 26, 2000·Trends in Ecology & Evolution·A Rokas, P W Holland
Dec 21, 2000·Current Opinion in Microbiology·D G Adams
Dec 23, 2000·Nucleic Acids Research·B L MaidakJ M Tiedje
Jun 20, 2001·International Journal of Systematic and Evolutionary Microbiology·A Ben AliY Van de Peer
Jan 5, 2002·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·T KanekoS Tabata
Mar 2, 2002·Applied and Environmental Microbiology·Gabrielle RocapSallie W Chisholm
Apr 6, 2002·Bioinformatics·Heiko A SchmidtArndt von Haeseler
Sep 6, 2002·Nature·Aharon Oren, Erko Stackebrandt
Sep 21, 2002·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yasukazu NakamuraSatoshi Tabata
Nov 26, 2002·Molecular Biology and Evolution·J Peter GogartenJeffrey G Lawrence
Nov 26, 2002·Science·Jason RaymondRobert E Blankenship
Mar 6, 2003·Genome Research·J Kirk HarrisNorman R Pace
Aug 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Alexis DufresneWolfgang R Hess
Aug 15, 2003·Nature·B PalenikJ Waterbury
Sep 2, 2003·The Journal of General and Applied Microbiology·Pil-Soo Seo, Akira Yokota
Oct 1, 2003·Proteins·Naomi Siew, Daniel Fischer
Nov 19, 2003·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yasukazu NakamuraSatoshi Tabata
Nov 19, 2003·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yasukazu NakamuraSatoshi Tabata
Dec 4, 2003·Molecular Microbiology·Jonathan CaspiShmuel Pietrokovski
Dec 6, 2003·International Journal of Systematic and Evolutionary Microbiology·Radhey S GuptaVanessa Johari
Mar 17, 2004·PLoS Biology·Richard J Roberts
Sep 25, 2004·International Journal of Systematic and Evolutionary Microbiology·Aharon Oren
Oct 14, 2004·Nucleic Acids Research·Michael Y Galperin, Eugene V Koonin
Nov 25, 2004·European Journal of Biochemistry·Masakazu SugishimaKeiichi Fukuyama
Feb 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ziheng Yang
Apr 1, 2005·PLoS Biology·Emmanuelle LeratNancy A Moran
Jul 15, 2005·Molecular Biology and Evolution·Gang FangAntoine Danchin
Sep 3, 2005·Nature Reviews. Microbiology·J Peter Gogarten, Jeffrey P Townsend
Mar 4, 2006·Science·Francesca D CiccarelliPeer Bork
Aug 23, 2006·Proceedings of the National Academy of Sciences of the United States of America·Armen Y MulkidjanianMichael Y Galperin
Aug 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Brian PalenikIan T Paulsen

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Citations

Aug 17, 2010·Antonie van Leeuwenhoek·Radhey S Gupta, Ali Shami
Apr 20, 2011·Antonie van Leeuwenhoek·Radhey S Gupta, Vaibhav Bhandari
Nov 4, 2011·Antonie van Leeuwenhoek·Beile Gao, Radhey S Gupta
Sep 19, 2012·Antonie van Leeuwenhoek·Danish MemonPramod P Wangikar
Apr 26, 2011·The Journal of Biological Chemistry·Steven J KarpowiczSabeeha S Merchant
Jun 10, 2011·Molecular Biology and Evolution·Alexis Criscuolo, Simonetta Gribaldo
Dec 1, 2011·Nucleic Acids Research·Zheng ZhangHui Liu
Mar 7, 2012·Microbiology and Molecular Biology Reviews : MMBR·Beile Gao, Radhey S Gupta
Jul 2, 2011·BMC Evolutionary Biology·John LarssonBirgitta Bergman
Oct 6, 2010·BMC Genomics·Shan LiZhengchang Su
Aug 17, 2012·BMC Microbiology·Bettina E SchirrmeisterHomayoun C Bagheri
Feb 25, 2014·Systematic Biology·Joel SjöstrandJens Lagergren
Mar 10, 2015·Life·Nils Schuergers, Annegret Wilde
Aug 29, 2014·Environmental Science & Technology·Shirley Y WongHerb E Schellhorn
Mar 29, 2014·International Journal of Systematic and Evolutionary Microbiology·Dasha A Ravinesan, Radhey S Gupta
Apr 9, 2015·Frontiers in Microbiology·Stefan SimmEnrico Schleiff
May 18, 2016·Molecular Biology and Evolution·Seyed Alireza Zamani-DahajPaul G Higgs
Oct 26, 2016·Biochimica Et Biophysica Acta·Sebastian VeitSascha Rexroth
Nov 9, 2016·Current Biology : CB·R Gary Sawers
Mar 12, 2020·Bioscience, Biotechnology, and Biochemistry·Satoru Watanabe
Jul 24, 2020·Environmental Microbiology·Vinícius W SalazarFabiano L Thompson
Jan 7, 2011·FEMS Microbiology Letters·Julia Domínguez-EscobarLuisa I Falcón
May 26, 2017·Frontiers in Microbiology·Danillo O AlvarengaAlessandro M Varani

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Datasets Mentioned

BETA
MIT9303

Methods Mentioned

BETA
light harvesting
PCR

Software Mentioned

- PUZZLE
ClustalX
Gblocks
blast
Blastp
TREECON
TREE
DWM

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