@ARTICLE{TreeBASE2Ref27392,
author = {Willie Anderson dos Santos Vieira and Wal?ria G Lima and Eduardo Souza Nascimento and Sami Jorge Michereff and Marcos P. S. Camara and Vinson P Doyle},
title = {The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa},
year = {2017},
keywords = {Alignment uncertainty, anthracnose, culture media, genealogical concordance phylogenetic species recognition, phylogenetic signal, 1 new taxon},
doi = {10.1080/00275514.2017.1418577},
url = {http://www.tandfonline.com/doi/full/10.1080/00275514.2017.1418577},
pmid = {},
journal = {Mycologia},
volume = {109},
number = {6},
pages = {912--934},
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.}
}
Citation for Study 21262
Citation title:
"The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa".
Study name:
"The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa".
This study is part of submission 21262
(Status: Published).
Citation
Vieira W.D., Lima W.G., Nascimento E.S., Michereff S.J., Camara M.P., & Doyle V.P. 2017. The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa. Mycologia, 109(6): 912-934.
Authors
-
Vieira W.D.
(submitter)
5581997315637
-
Lima W.G.
-
Nascimento E.S.
-
Michereff S.J.
-
Camara M.P.
-
Doyle V.P.
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
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S21262
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref27392,
author = {Willie Anderson dos Santos Vieira and Wal?ria G Lima and Eduardo Souza Nascimento and Sami Jorge Michereff and Marcos P. S. Camara and Vinson P Doyle},
title = {The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa},
year = {2017},
keywords = {Alignment uncertainty, anthracnose, culture media, genealogical concordance phylogenetic species recognition, phylogenetic signal, 1 new taxon},
doi = {10.1080/00275514.2017.1418577},
url = {http://www.tandfonline.com/doi/full/10.1080/00275514.2017.1418577},
pmid = {},
journal = {Mycologia},
volume = {109},
number = {6},
pages = {912--934},
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.}
}
- Show RIS reference
TY - JOUR
ID - 27392
AU - Vieira,Willie Anderson dos Santos
AU - Lima,Wal?ria G
AU - Nascimento,Eduardo Souza
AU - Michereff,Sami Jorge
AU - Camara,Marcos P. S.
AU - Doyle,Vinson P
T1 - The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa
PY - 2017
KW - Alignment uncertainty
KW - anthracnose
KW - culture media
KW - genealogical concordance phylogenetic species recognition
KW - phylogenetic signal
KW - 1 new taxon
UR - http://www.tandfonline.com/doi/full/10.1080/00275514.2017.1418577
N2 - 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.
L3 - 10.1080/00275514.2017.1418577
JF - Mycologia
VL - 109
IS - 6
SP - 912
EP - 934
ER -