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Citation for Study 17084

Citation title: "Diversity and movement of indoor Alternaria alternata across the mainland USA".

Study name: "Diversity and movement of indoor Alternaria alternata across the mainland USA".

This study is part of submission 17084 (Status: Published).

Citation

Woudenberg J.H., Van der merwe N.A., Jurjevic Z., Groenewald J.Z., & Crous P.W. 2015. Diversity and movement of indoor Alternaria alternata across the mainland USA. Fungal Genetics and Biology, 81: 62-72.

Authors

• Woudenberg J.H. (submitter)
• Van der merwe N.A.
• Jurjevic Z.
• Groenewald J.Z. +31302122600
• Crous P.W.

Abstract

Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration. However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or population genetic approach to investigate their movement. Therefore, the aim of the current study was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination, using these approaches. Alternaria isolates collected throughout the USA were identified using ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented 98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium (2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations to represent four quadrants of the USA. Forty-four isolates representing the south-western quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of gene flow was detected between the south-eastern (32 isolates) and south-western quadrants. Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.

Keywords

Microsatellites; population genetics; phylogeographic study; recombination

External links

• DOI: 10.1016/j.fgb.2015.05.003
• PMID: 26004989
• Other URL: http://www.sciencedirect.com/science/article/pii/S1087184515000997

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S17084
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24174,
  	 author = {Joyce H.C. Woudenberg and Nicolaas A Van der Merwe and Zeljko  Jurjevic and  Johannes (Ewald) Zacharias Groenewald and Pedro W. Crous},
  	 title = {Diversity and movement of indoor Alternaria alternata across the mainland USA},
  	 year = {2015},
  	 keywords = {Microsatellites; population genetics; phylogeographic study; recombination},
  	 doi = {10.1016/j.fgb.2015.05.003},
  	 url = {http://www.sciencedirect.com/science/article/pii/S1087184515000997},
  	 pmid = {26004989},
  	 journal = {Fungal Genetics and Biology},
  	 volume = {81},
  	 number = {},
  	 pages = {62--72},
  	 abstract = {Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration. However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or population genetic approach to investigate their movement. Therefore, the aim of the current study was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination, using these approaches. Alternaria isolates collected throughout the USA were identified using ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented 98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium (2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations to represent four quadrants of the USA. Forty-four isolates representing the south-western quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of gene flow was detected between the south-eastern (32 isolates) and south-western quadrants. Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24174
  AU  - Woudenberg,Joyce H.C.
  AU  - Van der Merwe,Nicolaas A
  AU  - Jurjevic,Zeljko 
  AU  - Groenewald, Johannes (Ewald) Zacharias
  AU  - Crous,Pedro W.
  T1  - Diversity and movement of indoor Alternaria alternata across the mainland USA
  PY  - 2015
  KW  - Microsatellites; population genetics; phylogeographic study; recombination
  UR  - http://www.sciencedirect.com/science/article/pii/S1087184515000997
  N2  - Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration. However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or population genetic approach to investigate their movement. Therefore, the aim of the current study was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination, using these approaches. Alternaria isolates collected throughout the USA were identified using ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented 98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium (2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations to represent four quadrants of the USA. Forty-four isolates representing the south-western quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of gene flow was detected between the south-eastern (32 isolates) and south-western quadrants. Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.
  L3  - 10.1016/j.fgb.2015.05.003
  JF  - Fungal Genetics and Biology
  VL  - 81
  IS  - 
  SP  - 62
  EP  - 72
  ER  -