Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene

Whole genome sequencing and annotation of Pseudocercospora abelmoschi, a causal agent of black leaf mould of okra

Pseudocercospora abelmoschi causes black mould on the leaves of okra. The disease is prevalent post-rainy season when high moisture and warm temperatures prevail. Severe defoliation is observed during favourable environments, leading to a significant loss in productivity. Based on the importance of the pathogen agriculturally, the P. abelmoschi isolate Cer 86 - 18 (MCC:9491) was selected for genome sequencing. The genome assembly of P. abelmoschi resulted in a genome of 31.90 Mb with an overall GC content of 54.26%. Quantitative genome assessment using BUSCO (Benchmarking Universal Single-Copy Orthologs) identified 1,664 (97.53%) complete BUSCOs, reflecting a high representation of conserved genes with minimal duplication and strong orthologous uniqueness. Gene prediction analysis identified 11,325 protein-coding genes, of which 3,857 were annotated using the KEGG database. As per analyses, 410 genes were predicted to encode carbohydrate-active enzymes, whereas 369 genes were predicted to encode peptidases. Eighteen gene clusters involved in secondary metabolite biosynthesis were also identified. A total of 143 proteins were predicted to be effectors using the in-silico pipeline. This is the first report on the genome organisation of P. abelmoschi. This study was designed to address this gap by enhancing our understanding of the genome organisation of P. abelmoschi and gene annotation, thereby paving the way for functional genomics studies, such as identifying virulence genes to aid in resistance breeding. Also, this genome could be another addition to the available genomic resources of the genus Pseudocercospora and can provide valuable insights into host-pathogen interactions and evolutionary relationships.

From Chaos Comes Order: Genetics and Genome Biology of Arbuscular Mycorrhizal Fungi

Arbuscular mycorrhizal fungi (AMF) are obligate mutualists that can enhance nutrition and growth of their plant hosts while providing protection against pathogens. AMF produce spores and hyphal networks that can carry thousands of nuclei in a continuous cytoplasm, with no evidence of sexual reproduction. This review examines the impact of genomic technologies on our view of AMF genetics and evolution. We highlight how the genetics, nuclear dynamics, and epigenetics of these prominent symbionts follow trends preserved in distant multinucleate fungal relatives. We also propose new avenues of research to improve our understanding of their nuclear biology and their intricate genetic interactions with plant hosts.

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.