A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

D. Udayanga, X. Liu, P.W. Crous, E.H.C. McKenzie, E. Chukeatirote, K.D. Hyde

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Abstract

The genus Diaporthe (Phomopsis) includes important plant pathogenic fungi with wide host ranges and geographic distributions. In the present study, phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS, and partial sequences from the translation elongation factor 1-a (EF 1-a), ß tubulin (TUB) and calmodulin (CAL) molecular markers. DNA sequences of available ex-type cultures have been included, providing a multi-locus backbone tree for future studies on Diaporthe. Four utilizable loci were analyzed individually and in combination, and ITS, EF 1-a and multi-locus phylogenetic trees are presented. The phylogenetic tree inferred by combined analysis of four loci provided the best resolution for species as compared to single gene analysis. Notes are provided for nine species previously known in Phomopsis that are transferred to Diaporthe in the present study. The unraveling of cryptic species complexes of Diaporthe based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) is emphasized.
Original languageEnglish
Pages (from-to)157-171
JournalFungal Diversity
Volume56
Issue number1
DOIs
Publication statusPublished - 2012

Keywords

  • multiple sequence alignment
  • plant-pathogenic fungi
  • species concepts
  • south-africa
  • primer sets
  • genes
  • phaseolorum
  • longicolla
  • pcr
  • phylogeography

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    Udayanga, D., Liu, X., Crous, P. W., McKenzie, E. H. C., Chukeatirote, E., & Hyde, K. D. (2012). A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Diversity, 56(1), 157-171. https://doi.org/10.1007/s13225-012-0190-9