Pan-genomics of fungi and its applications

Kato, Rodrigo Bentes; Jaiswal, Arun Kumar; Tiwari, Sandeep; Barh, Debmalya; Azevedo, Vasco; Goés-Neto, Aristóteles

doi:10.1016/b978-0-12-817076-2.00012-3

Cited by 4 publications

(3 citation statements)

References 33 publications

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“…doe. gov/ fungi) has largely facilitated and stimulated many molecular studies concerning several aspects of the fundamental biology and physiology of fungi, including their phylogeny, evolution, and adaptation [45][46][47]. The first Sporothrix genome, that of S. schenckii, was sequenced and deposited in Genbank in 2013 (GenBank: GCA_000474925.1), and since then the genomes of all pathogenic species have been sequenced and released [12,15] thereby providing useful background genetic information for future gene-specific analyses.…”

Section: Discussionmentioning

confidence: 99%

Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade

Giosa

Wei

et al. 2022

BMC Genomics

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Background The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of disease-causing species have already been sequenced and annotated but no comprehensive genomic resources for environmental Sporothrix species are available, thus limiting our understanding of the evolutionary origin of virulence-related genes and pathogenicity. Result The genome assembly of four environmental Sporothrix species resulted in genome size of ~ 30.9 Mbp in Sporothrix phasma, ~ 35 Mbp in S. curviconia, ~ 38.7 Mbp in S. protearum, and ~ 39 Mbp in S. variecibatus, with a variable gene content, ranging from 8142 (S. phasma) to 9502 (S. variecibatus). The analysis of mobile genetic elements showed significant differences in the content of transposable elements within the sequenced genomes, with the genome of S. phasma lacking several class I and class II transposons, compared to the other Sporothrix genomes investigated. Moreover, the comparative analysis of orthologous genes shared by clinical and environmental Sporothrix genomes revealed the presence of 3622 orthogroups shared by all species, whereas over 4200 genes were species-specific single-copy gene products. Carbohydrate-active enzyme analysis revealed a total of 2608 protein-coding genes containing single and/or multiple CAZy domains, resulting in no statistically significant differences among pathogenic and environmental species. Nevertheless, some families were not found in clinical species. Furthermore, for each sequenced Sporothrix species, the mitochondrial genomes was assembled in a single circular DNA molecule, ranging from 25,765 bp (S. variecibatus) to 58,395 bp (S. phasma). Conclusion In this study, we present four annotated genome assemblies generated using PacBio SMRT sequencing data from four environmental species: S. curviconia, S. phasma, S. protearum and S. variecibatus with the aim to provide a starting point for future comparative genome evolution studies addressing species diversification, ecological/host adaptation and origin of pathogenic lineages within the genus Sporothrix.

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Section: Discussionmentioning

confidence: 99%

Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade

Giosa

Wei

et al. 2022

BMC Genomics

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“…Additionally, the pan-genome provides enhanced insights into the presence/absence variation (PAV)based genome-wide association study (PAV-GWAS), establishing a possible association between the genotype and phenotype. To date, pan-genomes have been broadly used for population structure assessment, diversity analysis, and identification of important functional genes in humans [11] and plants [12][13][14][15][16][17][18], and also for the identification of novel pathogenic strains, or genes associated with infection in fungi [9,[19][20][21] and bacteria [22].…”

Section: Introductionmentioning

confidence: 99%

Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae

Bao

Wang

Chen

et al. 2022

JoF

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(1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus.

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“…One approach to better understand the genetic diversity and gene distribution within species is to combine comparative genomics with pan-genome analysis. Comparative genomics compares the genomic content of one species to another at micro- as well as macro-syntenic levels, based on gene annotation, the characterization of genome plasticity, and other evolutionary events, and resolves phylogenetic relationships [ 38 , 39 , 40 , 41 ]. While comparative genomic analysis can span kingdoms, pan-genome analysis was developed to narrow down the understanding of similarities and differences between strains or isolates of the same species or genus [ 42 , 43 , 44 , 45 , 46 ].…”

Section: Introductionmentioning

confidence: 99%

De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea

Ogaji

Lee

Sawbridge

et al. 2022

JoF

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Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.

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Pan-genomics of fungi and its applications

Cited by 4 publications

References 33 publications

Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade

Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade

Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae

De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea

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