Molecular Pathogens 2024, Vol.15, No.3, 155-169 http://microbescipublisher.com/index.php/mp 159 2019). Additionally, the mitochondrial genomes of PM pathogens, including P. xanthii, exhibit remarkable variation in size and nucleotide composition, further underscoring the genetic diversity within these species (Kim et al., 2019; Zaccaron and Stergiopoulos, 2021). Table 1 Summary of genome assemblies and gene annotations Assemblies and annotations Statistics Assembly Contigs 1 112 Total bases 209 067775 Average length 188 010.59 Minimum length 19987 Maximum length 2 325138 N5o 581 650 N(%) 0.00 GC (%) 44.25 Gene Genes 12834 Average gene length 2 418.79 Average exon length 425.23 Repeat elements 132 699 478 (63.41%) Gene coverage 14.83% BUSco 98.3%; C:745 [S:367, D:378], F:0, M:13, n:758 Annotations Blast-hits 10 461 (81.51%) Kyoto Encyclopedia of Genes and Genomes (KEGG) 7 375 (57.46%) Gene Ontology (GO) 8 529 (66.46%) No-hits 2 373 (18.49%) Candidate secrete effector proteins (CSEP) 455 Secreted proteins (SP) 690 Nonclassical secreted proteins (NCSP) 169 Cytochrome (CYP) 37 Carbohydrate-active enzymes (CAZY) 519 Table caption: This table presents the comprehensive results of the genome assembly and annotation process. It shows the total assembled genome size at 209.07 MB, with 63.41% comprised of repetitive elements, primarily long terminal repeats. A total of 12 834 genes were predicted using a combination of evidence-based, ab initio, and consensus gene modeling approaches. The pie chart illustrates the proportion of genes that match known sequences in the GenBank NR database, highlighting the genetic connectivity with other organisms (Adapted from Pérez-García et al., 2009). The genomic assembly and annotation described by Pérez-García et al. (2009) offer profound insights into the genetic composition and complexity of the organism. The use of long-read sequencing technologies, combined with a haplotype-aware assembler, has allowed for a detailed and comprehensive view of the genome. The high percentage of repetitive sequences and the identification of a substantial number of genes are indicative of a complex genome, which could involve significant regulatory mechanisms and adaptability features. Such genomic data are invaluable for further genetic studies, potentially leading to discoveries related to gene function, evolutionary biology, and biotechnological applications. The alignment of a significant portion of the genes with those in the GenBank NR database also provides a basis for comparative genomics, enhancing our understanding of gene conservation and divergence among related species 4.3 Comparative genomics: insights from other pathogenic fungi Comparative genomics has provided insights into the evolution and adaptation of PM fungi. For instance, the PM fungi have large genomes with a high content of repetitive DNA sequences, primarily composed of retrotransposons (Vela-Corcía et al., 2016; Kusch et al., 2023). These elements play a key role in shaping the genome architecture and contribute to the rapid evolution of the fungi by enabling them to overcome plant immunity and evolve fungicide resistance (Kusch et al., 2023). Comparative analysis of the mitochondrial
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