title: Application of the Apn2/MAT locus to improve the systematics of the Colletotrichum gloeosporioides complex: an example from coffee (Coffea spp.) hosts.
abstract: To improve phylogenetic resolution of the Colletotrichum gloeosporioides species complex we developed and tested the performance of a new set of primers for the Apn2/MAT locus with a case study of 22 isolates. These were isolated mainly from coffee plants and represent six divergent and well characterized species within the C. gloeosporioides complex. Following previous studies on this locus, we have generated sequence data from an expanded region (> 4600 bp), revealing increased phylogenetic informativeness when compared to other commonly used markers such as ITS, β-tub2 and GS. Within the Apn2/MAT locus the ApMAT marker alone was almost as informative in terms of phylogenetic resolution as a seven-gene concatenated dataset. Our results further revealed that gene-tree discordance may come to be a common issue in resolving evolutionary relationships in the C. gloeosporioides complex, highlighting the importance of multilocus approaches. The use of state-of-the-art data analysis techniques and a highly informative dataset as employed here may abate this issue and hopefully assist in disentangling the C. gloeosporioides complex.
authors.affiliation: Instituto de Investigação Científica Tropical, Quinta do Marquês, Oeiras, Portugal.
authors.forename: Diogo Nuno
authors.initials: DN
authors.lastname: Silva
authors.forename: Pedro
authors.initials: P
authors.lastname: Talhinhas
authors.forename: Vítor
authors.initials: V
authors.lastname: Várzea
authors.forename: Lei
authors.initials: L
authors.lastname: Cai
authors.forename: Octávio Salgueiro
authors.initials: OS
authors.lastname: Paulo
authors.forename: Dora
authors.initials: D
authors.lastname: Batista
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D040503:Coffea / Q000382:microbiology*; D020231:Colletotrichum / Q000145:classification* / Q000235:genetics; D017931:DNA Primers / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D005656:Fungal Proteins; D005819:Genetic Markers