title: Diversity and movement of indoor Alternaria alternata across the mainland USA.
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.
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; WUR, Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Electronic address: j.woudenberg@cbs.knaw.nl.
authors.forename: J H C
authors.initials: JH
authors.lastname: Woudenberg
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.
authors.forename: N A
authors.initials: NA
authors.lastname: van der Merwe
authors.affiliation: EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, USA.
authors.forename: Ž
authors.initials: Ž
authors.lastname: Jurjević
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: J Z
authors.initials: JZ
authors.lastname: Groenewald
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; WUR, Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.
authors.forename: P W
authors.initials: PW
authors.lastname: Crous
mesh_terms: D000528:Alternaria / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D060005:Genotyping Techniques; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) / Q000235:genetics; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques; D058974:Phylogeography; D011096:Polygalacturonase / Q000235:genetics; D017422:Sequence Analysis, DNA; D014481:United States
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating); D011096:Polygalacturonase
keywords: Microsatellites; Phylogeographic study; Population genetics; Recombination