Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches

Abstract

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

VARIATION IN AGGRESSIVENESS AND AFLP AMONG Alternaria solani ISOLATES FROM INDONESIA

“…Isolates obtained from contiguous tomato and potato fields such as in Margahayu, Lembang, could possibly originate from a tomato field infected with an adapted lineage to this host. Other studies in the USA, Brazil and Cuba found population subdivision according to the host of origin as detected by RAPD and/or AFLP markers (Weir et al 1998;Martinez et al 2004;Lourenço et al 2011) as well as by sequence analyses of ITS region of rDNA and the genes encoding glyceraldehyde-3-phosphate dehydrogenase (gpd), and Alt a1 (Lourenço et al 2009). …”

“…Previous studies revealed considerable variability among isolates with respect to morphology, physiology, biochemistry, aggressiveness and genetics (Bonde 1929;Henning and Alexander 1959;Petrunak and Christ 1992;Weir et al 1998;Castro et al 2000;Martinez et al 2004;van der Waals et al 2004;Varma et al 2006;Lourenço et al 2009;Lourenço Jr et al 2011;Weber and Halterman 2012;Meng et al 2015;Kumar et al 2016;Odilbekov et al 2016). Great variability in A. solani is unexpected, since the sexual stage of this pathogen is not known (Meng et al 2015).…”

“…The occurrence of differential aggressiveness among isolates has led to the conclusion for the presence of physiological races (Bonde 1929). However, the race concept in A. solani has not been widely accepted due to lack of characterized differential varieties (Chaerani and Voorrips 2006;Gannibal et al 2014;Adhikari et al 2017) Genetic variation within A. solani populations has been assessed using various molecular markers which included random amplified polymorphic DNA (RAPD) (Weir et al 1998;Varma et al 2006;Kumar et al 2008;Lourenço Jr et al 2011;Weber and Halterman 2012;Leiminger et al 2013), random amplified microsatellites (RAMS) (van der Waals et al 2004), amplified fragment length polymorphism (AFLP) (Martinez et al 2004;Lourenço Jr et al 2011;Odilbekov et al 2016), and simple sequence repeats (SSRs) (Meng et al 2015), as well as sequence analyses of A. solani genome portion (Lourenço et al 2009;Weber and Halterman 2012). Among different types of molecular markers, AFLP marker has become one of the major methods of choice for studies of genetic diversity because it does not require prior knowledge of genomic sequence and generates a large number of polymorphic loci in a single experiment (Martinez et al 2004;Odilbekov et al 2016).…”

PRODUCTIVE POTENTIAL OF THE CHERRY TOMATO GENOTYPE GROUP BEFORE INFECTION BY Alternaria tomatophila

“…Although the etiology of the disease has been traditionally attributed to the fungus Alternaria solani Sorauer (ROTEM, 1994), in 2000 a new species was described, Alternaria tomatophila Simmons, is commonly associated with the black spot lesions on tomato plants (SIMMONS, 2000;LOURENÇO et al, 2009). In Brazil, it was demonstrated that the fungus A. tomatophilia is the etiologic agent of the disease (RODRIGUES et al, 2010).…”

Plant-Derived Natural Products From the American Continent for the Control of Phytopathogenic Fungi: A Review

“…Might be responsible for esophageal cancer. Greco et al, 2012;Gambale et al, 1976;Pollock et al, 1982;Biggs et al, 1993;Biggs, 1995;Gamboa-Angulo et al, 2000;Gamboa-Angulo et al, 2002;Andersen et al, 2008;Andrew et al, 2009;Lourenco et al, 2009;Alexander et al, 2011;Díaz Dellavalle et al, 2011;Somma et al, 2011;Edin, 2012;Pavón-Moreno et al, 2012;Benavidez Rozo et al, 2013 Aspergillus brasiliensis, A. costaricaensis, A. flavus, A. lacticoffeatus, A. nidulans and A. niger. Chaetocin, penitrem A, and xanthocillin , tenuazonic acid, aflatoxin G2, aflatoxin B1 and B2, chaetoglobosin C, ochratoxin A and spinulosin.…”