title: The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies.
abstract: The Mucorales (Mucoromycotina) are one of the most ancient groups of fungi comprising ubiquitous, mostly saprotrophic organisms. The first comprehensive molecular studies 11 yr ago revealed the traditional classification scheme, mainly based on morphology, as highly artificial. Since then only single clades have been investigated in detail but a robust classification of the higher levels based on DNA data has not been published yet. Therefore we provide a classification based on a phylogenetic analysis of four molecular markers including the large and the small subunit of the ribosomal DNA, the partial actin gene and the partial gene for the translation elongation factor 1-alpha. The dataset comprises 201 isolates in 103 species and represents about one half of the currently accepted species in this order. Previous family concepts are reviewed and the family structure inferred from the multilocus phylogeny is introduced and discussed. Main differences between the current classification and preceding concepts affects the existing families Lichtheimiaceae and Cunninghamellaceae, as well as the genera Backusella and Lentamyces which recently obtained the status of families along with the Rhizopodaceae comprising Rhizopus, Sporodiniella and Syzygites. Compensatory base change analyses in the Lichtheimiaceae confirmed the lower level classification of Lichtheimia and Rhizomucor while genera such as Circinella or Syncephalastrum completely lacked compensatory base changes.
authors.affiliation: Institute of Microbiology, Department of Microbiology and Molecular Biology, University of Jena, Jena, Germany. ; Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena Microbial Resource Collection, Jena, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Hoffmann
authors.forename: J
authors.initials: J
authors.lastname: Pawłowska
authors.forename: G
authors.initials: G
authors.lastname: Walther
authors.forename: M
authors.initials: M
authors.lastname: Wrzosek
authors.forename: G S
authors.initials: GS
authors.lastname: de Hoog
authors.forename: G L
authors.initials: GL
authors.lastname: Benny
authors.forename: P M
authors.initials: PM
authors.lastname: Kirk
authors.forename: K
authors.initials: K
authors.lastname: Voigt
keywords: Mucorales; families; phylogeny
references.citation: J Appl Microbiol. 2005;98(4):789-805
references.pmid: 15752324
references.citation: BMC Evol Biol. 2006 Nov 22;6:99
references.pmid: 17121679
references.citation: Org Biomol Chem. 2010 Oct 7;8(19):4229-31
references.pmid: 20694270
references.citation: Curr Genet. 2008 Mar;53(3):129-37
references.pmid: 18183399
references.citation: Annu Rev Microbiol. 1983;37:575-601
references.pmid: 6357061
references.citation: Mycol Res. 2007 Oct;111(Pt 10):1169-83
references.pmid: 17997297
references.citation: Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6241-6
references.pmid: 22454494
references.citation: Persoonia. 2009 Dec;23:35-40
references.pmid: 20198159
references.citation: Phytopathology. 1997 Dec;87(12):1226-32
references.pmid: 18945022
references.citation: Acta Biol Hung. 2008 Sep;59(3):365-83
references.pmid: 18839703
references.citation: Microbiol Res. 2000 Sep;155(3):179-95
references.pmid: 11061186
references.citation: Mycologia. 2005 Jan-Feb;97(1):1-11
references.pmid: 16389951
references.citation: Mycol Res. 2007 May;111(Pt 5):509-47
references.pmid: 17572334
references.citation: J Biol Chem. 1984 May 25;259(10):6420-2
references.pmid: 6547137
references.citation: Clin Microbiol Infect. 2011 Dec;17(12):1859-67
references.pmid: 21199154
references.citation: Mycologia. 2005 May-Jun;97(3):725-9
references.pmid: 16392260
references.citation: Mycologia. 2012 Jul-Aug;104(4):835-44
references.pmid: 22453117
references.citation: J Clin Microbiol. 2010 Jun;48(6):2154-70
references.pmid: 20357218
references.citation: Nature. 2011 May 11;474(7350):200-3
references.pmid: 21562490
references.citation: Proc Natl Acad Sci U S A. 1979 Feb;76(2):615-9
references.pmid: 284385
references.citation: J Clin Microbiol. 2010 Dec;48(12):4410-6
references.pmid: 20926710
references.citation: Eukaryot Cell. 2009 Jan;8(1):88-95
references.pmid: 18931040
references.citation: J Clin Microbiol. 2012 Jan;50(1):66-75
references.pmid: 22075600
references.citation: Nature. 2008 Jan 10;451(7175):193-6
references.pmid: 18185588
references.citation: Clin Microbiol Rev. 1999 Jan;12(1):126-46
references.pmid: 9880478
references.citation: Plant Biol (Stuttg). 2009 Jul;11(4):537-54
references.pmid: 19538392
references.citation: Biosci Biotechnol Biochem. 2010;74(7):1325-31
references.pmid: 20622457
references.citation: Proc Natl Acad Sci U S A. 1926 Mar;12(3):202-7
references.pmid: 16576979
references.citation: Fungal Genet Biol. 2000 Oct;31(1):21-32
references.pmid: 11118132
references.citation: Enzyme Microb Technol. 2011 Apr 7;48(4-5):326-33
references.pmid: 22112945
references.citation: RNA. 2007 Sep;13(9):1469-72
references.pmid: 17652131
references.citation: Science. 1964 Nov 13;146(3646):925-7
references.pmid: 17777060
references.citation: Mycologia. 2008 Mar-Apr;100(2):259-74
references.pmid: 18592900
references.citation: Trends Genet. 2000 Jun;16(6):276-7
references.pmid: 10827456
references.citation: Persoonia. 2013 Jun;30:11-47
references.pmid: 24027345
references.citation: Biochemistry. 1989 May 2;28(9):4060-6
references.pmid: 2752007
references.citation: Fungal Biol. 2012 Jun;116(6):692-705
references.pmid: 22658314
references.citation: Mycologia. 2007 Sep-Oct;99(5):714-22
references.pmid: 18268905
references.citation: Microbiology (Reading). 1996 Sep;142 ( Pt 9):2647-54
references.pmid: 8828234
references.citation: Nature. 1967 Jul 8;215(5097):211-2
references.pmid: 6049132
references.citation: Mol Phylogenet Evol. 2004 Sep;32(3):1036-60
references.pmid: 15288074
references.citation: Microbiol Mol Biol Rev. 2010 Jun;74(2):298-340
references.pmid: 20508251
references.citation: Gene. 2001 May 30;270(1-2):113-20
references.pmid: 11404008
references.citation: PLoS One. 2010 Dec 09;5(12):e15273
references.pmid: 21151560
references.citation: Mycologia. 2006 Nov-Dec;98(6):872-84
references.pmid: 17486964
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6
references.pmid: 17962297
references.citation: Crit Rev Food Sci Nutr. 2005;45(7-8):623-44
references.pmid: 16371331
references.citation: J Bacteriol. 1962 Oct;84:829-40
references.pmid: 13969719
references.citation: FEMS Yeast Res. 2006 Dec;6(8):1213-20
references.pmid: 17156018
references.citation: Mycol Res. 2003 Mar;107(Pt 3):339-50
references.pmid: 12825503
references.citation: Phytochemistry. 2005 Jun;66(11):1358-65
references.pmid: 15913673
references.citation: Curr Genet. 1993;23(4):334-7
references.pmid: 8467531
references.citation: Am J Bot. 2002 Apr;89(4):688-98
references.pmid: 21665669
references.citation: Fungal Genet Biol. 2012 May;49(5):398-404
references.pmid: 22445959
references.citation: Clin Infect Dis. 2005 Sep 1;41(5):634-53
references.pmid: 16080086
references.citation: Rev Iberoam Micol. 2010 Jun 30;27(2):80-9
references.pmid: 20199897
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3901-6
references.pmid: 17360450
references.citation: Gene. 2005 Mar 28;348:33-44
references.pmid: 15777660
references.citation: Mycologia. 2011 Jan-Feb;103(1):36-44
references.pmid: 20943555
references.citation: IMA Fungus. 2011 Dec;2(2):173-5
references.pmid: 22679602
references.citation: Nature. 2006 Oct 19;443(7113):818-22
references.pmid: 17051209
references.citation: Biosci Biotechnol Biochem. 2006 Oct;70(10):2387-93
references.pmid: 17031057
references.citation: Eukaryot Cell. 2011 Nov;10(11):1485-91
references.pmid: 21908600
references.citation: Sabouraudia. 1980 Jun;18(2):115-21
references.pmid: 7423330