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Fungal genetic systems ideally combine molecular tools for genome manipulation and a sexual reproduction system to create an informative assortment of combinations of genomic modifications. When employing the sexual cycle to generate multi-mutants, the background genotype variations in the parents may result in progeny phenotypic variation obscuring the effects of combined mutations. Here, to mitigate this variation in Fusarium verticillioides, we generated a MAT1-2 strain that was near isogenic to the sequenced wild-type MAT1-1 strain, FGSC7600. This was accomplished by crossing FGSC7600 with the divergent wild-type MAT1-2 strain FGSC7603 followed by six sequential backcrosses (e.g., six generations) of MAT1-2 progeny to FGSC7600. We sequenced each generation and mapped recombination events. The parental cross involved twenty-six crossovers on nine of the eleven chromosomes. The dispensable chromosome 12, found in FGSC7603 but lacking in FGSC7600, was not present in the progeny post generation five. Inheritance of complete chromosomes without crossover was frequently observed. A deletion of approximately 140 kilobases, containing 54 predicted genes on chromosome 4, occurred in generation 4 and was retained in generation 5 indicating that these genes are dispensable for growth and both asexual and sexual reproduction. The final MAT1-2 strain TMRU10/35 is about 93% identical to FGSC7600. TMRU10/35 is available from the Fungal Genetics Stock Center as FGSC27326 and from the ARS Culture Collection as NRRL64809. [ABSTRACT FROM AUTHOR]

Gene duplication and polyploidy are some of the most important, yet underappreciated, evolutionary forces that have shaped all flowering plants on earth, and the crop plants that enable human economic activity are prime exemplars of duplication in action. Polyploidy involves an immediate doubling, tripling, or more of a genome, often followed by drastic chromosomal reorganization or a reduction back to diploidy, and has occurred many times in the history of most characterized plant genomes. Understanding how duplication shapes plant genomes is critical for understanding how to feed a growing and hungry global human population. Of particular importance are legumes, one of the largest plant families on earth, often noted for their nitrogen fixation abilities and high nutritional value due to their protein content. Among these Papilionoid (Faboideae) legume crops are alfalfa, soybean, peanut, and common bean. All of these have experienced polyploidy events somewhere in their history, some ancient (60 My or more) and some very recent (e.g., ~10,000 years ago in peanut). The modes by which these polyploidies arose, whether from divergent genomes coming together (allopolyploidy), or identical or similar genomes duplicating (autopolyploidy), can affect their evolution, domestication, and improvement considerably, whether by generating new functional diversity or driving speciation. Appreciating the indelible mark polyploidy and duplication leave on these legume genomes will enable a better understanding of the molecular biology, breeding, and agronomy of these critical crops. [ABSTRACT FROM AUTHOR]

Background: Single-stranded non-protein coding small RNAs, 18-25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have been reported for the detection of genetic diversity or sequence variation in soybean, one of the most important legume crops in worldwide for seed protein and oil content. Recently, with the available of public genomic databases, there has been a shift from the labor-intensive development of PCR-based markers to sequence-based genotyping and the development of functional markers within genes, often coupled with the use of RNA information. But thus far miRNA-based markers have been only developed in rice and tobacco. Here we report the first functional molecular miRNA marker, miR1511-InDel, in soybean for a specific single copy locus used to assess genetic variation in domesticated soybean (Glycine max [L.] Merr) and its wild progenitor (Glycine soja Sieb. & Zucc.). Results: We genotyped a total of 1,669 accessions of domesticated soybean (G. max) and its wild progenitor G. soja which are native throughout the China and parts of Korea, Japan and Russia. The results indicate that the miR1511 locus is distributed in cultivated soybean and has three alleles in annual wild soybean. Based on this result, we proposed that miR-InDel marker technology can be used to assess genetic variation. The inclusion of geo-reference data with miR1511-InDel marker data corroborated that accessions from the Yellow River basin (Huanghuai) exhibited high genetic diversity which provides more molecular evidence for gene diversity in annual wild soybean and domestication of soybean. Conclusions: These results provide evidence for the use of RNA marker, miRNA1511-InDel, as a soybean-specific functional maker for the study of genetic diversity, genotyping of germplasm and evolution studies. This is also the first report of functional marker developed from soybean miRNA located within the functional region of pre-miRNA1511. [ABSTRACT FROM AUTHOR]

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., (Copyright © 2020 Fountain et al.)