The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa

ABSTRACT

Developing a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites. Similarly, the choice of phylogenetic marker affects the delimitation of species boundaries, particularly if low phylogenetic signal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogenetic informativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase (APN2), intergenic spacer (IGS) between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamine synthetase (GS), β-tubulin (TUB2), and a new marker, the intergenic spacer between GAPDH and an hypothetical protein (GAP2-IGS). Cornmeal agar minimizes the variance in conidial dimensions compared with potato dextrose agar and synthetic nutrient-poor agar, such that species are more readily distinguishable based on phenotypic differences. We apply these insights to investigate the diversity of Colletotrichum species associated with banana anthracnose in Brazil and report C. musae, C. tropicale, C. theobromicola, and C. siamense in association with banana anthracnose. One lineage did not cluster with any previously described species and is described here as C. chrysophilum.

KEYWORDS:

• Alignment uncertainty
• anthracnose
• culture media
• genealogical concordance phylogenetic species recognition
• phylogenetic signal
• 1 new taxon

ACKNOWLEDGMENTS

The authors would like to thank the staff of the CMM culture collection and Dr. Ailton Reis (Empresa Brasileira de Perquisa Agropecuária [Embrapa], Embrapa Hortaliças, Brazil) for the provision of cultures; Josiene S. Veloso and Mariote S. B. Netto (Laboratory of Mycology, Departament of Agronomy, Universidade Federal Rural de Pernambuco [UFRPE], Recife, Brazil), and Sebastian Albu, Haley Hutchins, Caroline Baer, and Candace Hernandez (Louisiana State University, Baton Rouge, Louisiana, USA) for laboratory support. The authors thank Stephen Rehner for valuable discussion and helpful comments that improved the quality of the manuscript. The authors would also like to acknowledge the computational resources provided by High Performance Computing at Louisiana State University (www.hpc.lsu.edu).

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Additional information

Funding

This study was funded by “Fundação de Amparo a Ciência e Tecnologia de Pernambuco (FACEPE)” (process number APQ-0790-5.01/12), the “Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)” (universal number 442279/2014-0), and the Louisiana State University AgCenter. Willie A. S. Vieira acknowledges “Ciência sem Fronteiras, CNPq” (process number 99999.006035/2014-00), FACEPE (process number IBPG-0855-5.01/11), and the Department of Plant Pathology and Crop Physiology (Louisiana State University AgCenter, Baton Rouge, Louisiana, USA) for financial support and the opportunity for student exchange. Marcos P. S. Câmara and Sami J. Michereff acknowledge CNPq for the research fellowship. Vinson P. Doyle acknowledges financial support from the Louisiana State Board of Regents (LEQSF-2016-19-RD-A-01) and the Louisiana State University AgCenter.