Genome Sequence Resources for the Maize Pathogen Fusarium temperatum Isolated in Poland

Reference-based read clustering improves the de novo genome assembly of microbial strains

Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving de novo microbial genome assembly, by accurately estimating read proximity using multiple reference genomes. The performance of RBRC was confirmed by simulation-based evaluation in terms of assembly contiguity and the number of misassemblies, and was successfully applied to existing fungal and bacterial genomes by improving the quality of the assemblies without using additional sequencing data. RBRC is a very useful read-clustering algorithm that can be used (i) for generating high-quality genome assemblies of microbial strains when genome assemblies of related strains are available, and (ii) for upgrading existing microbial genome assemblies when the generation of additional sequencing data, such as long reads, is difficult.

Influence of Endosperm Starch Composition on Maize Response to Fusarium temperatum Scaufl. & Munaut

Fusarium temperatum Scaufl. & Munaut is a newly described taxon belonging to the Fusarium fujikuroi species complex (FFSC) and a frequent causative factor of maize ear rot. The aim of the present study was to determine the responses to the disease in maize populations differing in endosperm features that were classified to flint, dent, and a group of plants with intermediate kernel characteristics. In inoculation studies, substantial variation of host response to the fungus was found among the tested maize types. The dent-type kernels contained significantly less amylose (28.27%) and exhibited significantly higher rates of infection (I_FER = 2.10) and contamination by beauvericin (7.40 mg kg⁻¹) than plants of the flint maize subpopulation. The study documents a significant positive correlation between the Fusarium ear rot intensity (I_FER) and ergosterol content (the R value ranged from 0.396 in 2015 to 0.735 in 2018) and between I_FER and the presence of beauvericin (the R value ranged from 0.364 in 2015 to 0.785 in 2017). The negative correlation between (I_FER) and amylose content (ranging from R = −0.303 to R= −0.180) stresses the role of the endosperm starch composition in the kernel resistance to Fusarium ear rot. The conducted study indicated that the risk of kernel infection and contamination with fungal metabolites (beauvericin and ergosterol) was associated with the maize type kernels.