Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus.
The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.
['van der Nest|Magriet A|MA|', 'Steenkamp|Emma T|ET|', 'Roodt|Danielle|D|', 'Soal|Nicole C|NC|', 'Palmer|Marike|M|', 'Chan|Wai-Yin|WY|', 'Wilken|P Markus|PM|', 'Duong|Tuan A|TA|', 'Naidoo|Kershney|K|', 'Santana|Quentin C|QC|', 'Trollip|Conrad|C|', 'De Vos|Lieschen|L|', 'van Wyk|Stephanie|S|', 'McTaggart|Alistair R|AR|', 'Wingfield|Michael J|MJ|', 'Wingfield|Brenda D|BD|']
D000349:Africa D001203:Ascomycota D019295:Computational Biology D019143:Evolution, Molecular D023061:Gene Order D014644:Genetic Variation D016681:Genome, Fungal D023281:Genomics D059014:High-Throughput Nucleotide Sequencing D020071:Interspersed Repetitive Sequences D010935:Plant Diseases D026801:Synteny D014197:Trees
Transposable elements Adaptation Ceratocystis wilt Core and accessory genomes Host jumps Pathogenomics