Comparative genomics of the nuclear and mitochondrial genomes of fungal tree pathogens causing Dothistroma needle blight

Abstract

The steps for managing the effect and impact of disease-causing pathogens involves understanding how new pathogens arise, their adaptation strategies, and evolutionary mechanisms. Evolution, speciation, and natural selection are some of the strategies used by most pathogens to adapt to new environments and become more virulent and hence overcome human, biotic and abiotic factors aimed at their eradication. The use of bioinformatics tools and, specifically, comparative genomics, is one of the methods employed to understand the evolution of pathogens, by studying variations amongst pathogen genomes and how they impact pathogen survival. The Dothistroma needle blight pathogen species show similar symptoms on their hosts but differ in host ranges and geographical distribution. In this study, using a comparative genomics approach, variations in the nuclear and mitochondrial genomes between D. pini, D. septosporum, and Dothistroma strains from Guatemala were discovered. This study is the first to generate a reference genome for D. pini that can be used for downstream genomic studies, and it is the first to study the mitochondrial genomes of the Dothistroma sp. The Dothistroma pathogens differ in nuclear genome sizes ranging between 29 Mb in D. septosporum to 33 Mb for the Dothistroma strains from Guatemala. The D. pini genome was characterised with the highest number of repeats, especially simple repeats (1.01 – 1.05% of the genome), when compared to Dothistroma strains from Guatemala (0.82 %) and D. septosporum (0.8%). The larger number of repeats may have contributed to the large genome sizes of D. pini and Dothistroma strains from Guatemala. All the pathogen species contained the complete dothistromin gene clusters with all the genes represented in their respective clusters. Additionally, all the dothistromin genes were expressed in D. pini as seen in RNA data generated in this study. Variations in the dothistromin cluster were seen in gene synteny as gene rearrangements, indels, and inversions across the species. All the strains had six CAZyme families represented with slightly more CAZymes observed in the Dothistroma strains from Guatemala. Conclusively, D. pini and Dothistroma strains from Guatemala are also hemibiotrophic, as has been reported for D. septosporum. Although, the isolates from Guatemala had a higher cell wall degrading capacity, the D. pini strains had the least number of secondary metabolites (SM) genes and lacked the indole genes which is involved in the synthesis of secondary metabolites. They were, however, the only ones with the betalactone SM genes. Comparison of orthologous genes showed that all the strains shared 7 433 orthogroups with D. pini having the largest number of species-specific orthogroups. Based on the calculations of average nucleotide identity and the phylogenetic analyses, there is strong support for the isolates from Guatemala to be recognised as a new species. These strains are also more closely related to D. pini than D. septosporum. Whole genome alignment shows that D. pini has gene sparse accessory scaffolds which are repeat rich and that were not found in D. septosporum. This was also associated with the large genome size observed in D. pini. The mitogenomes of D. septosporum, D. pini and Dothistroma strains from Guatemala contained all 14 protein-coding genes normally found in fungal mitochondria. They also had the long and short ribosomal RNA and several tRNA clusters. There were variations in genome sizes, number and location of intron ORF and sizes of intergenic regions. These were associated with the impact of HEGs and the presence of tandem repeats, dispersed repeats, and simple repeats. Other variations in the mitochondrial genomes of the three species were seen in the distribution of repeats, and synteny of protein-coding genes. The nad3 gene was duplicated only in the D. septosporum strains while the cob gene was fragmented in the Dothistroma strains from Guatemala. The Dothistroma mitochondrial phylogeny supported the distinction of three species, however, the mitogenomes of D. pini and D. septosporum were more closely related to each other than those of the Guatemala strains. The reasons behind the difference in the phylogenetic topology between nuclear and mitochondrial genomes will need further investigation.