Biocontrol strain Aspergillus flavus WRRL 1519 has differences in chromosomal organization and an increased number of transposon-like elements compared to other strains

Investigating the origin of subtelomeric and centromeric AT-rich elements in Aspergillus flavus

An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) in non-centromeric regions uncovered two major categories of ATEs. The first category is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs; Classes B, C, D, and E). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second category consists of a conserved set of novel subtelomeric ATE repeats (Classes A, G, G, H, I and J) which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. A third category of ATEs consists of ~100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.

Advanced mycotoxin control and decontamination techniques in view of an increased aflatoxin risk in Europe due to climate change

Aflatoxins are toxic secondary metabolites produced by Aspergillus spp. found in staple food and feed commodities worldwide. Aflatoxins are carcinogenic, teratogenic, and mutagenic, and pose a serious threat to the health of both humans and animals. The global economy and trade are significantly affected as well. Various models and datasets related to aflatoxins in maize have been developed and used but have not yet been linked. The prevention of crop loss due to aflatoxin contamination is complex and challenging. Hence, the set-up of advanced decontamination is crucial to cope with the challenge of climate change, growing population, unstable political scenarios, and food security problems also in European countries. After harvest, decontamination methods can be applied during transport, storage, or processing, but their application for aflatoxin reduction is still limited. Therefore, this review aims to investigate the effects of environmental factors on aflatoxin production because of climate change and to critically discuss the present-day and novel decontamination techniques to unravel gaps and limitations to propose them as a tool to tackle an increased aflatoxin risk in Europe.

Genetic map and heritability of Aspergillus flavus

The carcinogenic aflatoxins are a human health concern as well as an economic burden to corn, peanut and other crops grown within the United States and globally. Aflatoxins are produced by fungi species in Aspergillus section Flavi, primarily Aspergillus flavus. Though previously thought of as only asexual, A. flavus has recently been found to undergo sexual reproduction both in laboratory crosses and in the field. To elucidate the consequences of genetic exchange through a single generation of the sexual cycle within A. flavus, we constructed genetic maps based on three mapping populations, each composed of the parental strains and approximately 70 F1 progeny. Genome-wide data using double digest Restriction Associated DNA sequencing identified 496, 811, and 576 significant polymorphisms differentiating parents across eight linkage groups; these polymorphisms served as markers. Average spacing between marker loci was 3.1, 2.1, and 3.5 map units and overall map length was 1504.4, 1669.2, and 2001.3 cM. Recombination was non-randomly distributed across chromosomes with an average rate of recombination of about 46.81 cM per Mbp. We showed inheritance of mitochondrial loci from the sclerotial (female) parent in crosses, whereas nuclear loci showed a 1:1 segregation ratio from both parents. The linkage map will be useful in QTL analyses to identify traits that increase sexual fertility in A. flavus and modulate aflatoxin production, both of which have significant implications for sustainable reduction of aflatoxin contamination using biological control agents.

Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production

Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae However, less progress has been made for A. flavus As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference-grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 60 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.