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Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).

Publication ,  Journal Article
Hofstetter, V; Miadlikowska, J; Kauff, F; Lutzoni, F
Published in: Molecular phylogenetics and evolution
July 2007

The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.

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Published In

Molecular phylogenetics and evolution

DOI

EISSN

1095-9513

ISSN

1055-7903

Publication Date

July 2007

Volume

44

Issue

1

Start / End Page

412 / 426

Related Subject Headings

  • Sequence Analysis, DNA
  • Phylogeny
  • Open Reading Frames
  • Molecular Sequence Data
  • Likelihood Functions
  • Evolutionary Biology
  • DNA, Ribosomal
  • DNA, Fungal
  • Ascomycota
  • 3109 Zoology
 

Citation

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Hofstetter, V., Miadlikowska, J., Kauff, F., & Lutzoni, F. (2007). Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Molecular Phylogenetics and Evolution, 44(1), 412–426. https://doi.org/10.1016/j.ympev.2006.10.016
Hofstetter, Valérie, Jolanta Miadlikowska, Frank Kauff, and François Lutzoni. “Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).Molecular Phylogenetics and Evolution 44, no. 1 (July 2007): 412–26. https://doi.org/10.1016/j.ympev.2006.10.016.
Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Molecular phylogenetics and evolution. 2007 Jul;44(1):412–26.
Hofstetter, Valérie, et al. “Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).Molecular Phylogenetics and Evolution, vol. 44, no. 1, July 2007, pp. 412–26. Epmc, doi:10.1016/j.ympev.2006.10.016.
Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Molecular phylogenetics and evolution. 2007 Jul;44(1):412–426.
Journal cover image

Published In

Molecular phylogenetics and evolution

DOI

EISSN

1095-9513

ISSN

1055-7903

Publication Date

July 2007

Volume

44

Issue

1

Start / End Page

412 / 426

Related Subject Headings

  • Sequence Analysis, DNA
  • Phylogeny
  • Open Reading Frames
  • Molecular Sequence Data
  • Likelihood Functions
  • Evolutionary Biology
  • DNA, Ribosomal
  • DNA, Fungal
  • Ascomycota
  • 3109 Zoology