Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Olarte, Rodrigo A.; Menke, Jon; Zhang, Ying; Sullivan, Shawn; Slot, Jason C.; Huang, Yinyin; Badalamenti, Jonathan P.; Quandt, C. Alisha; Spatafora, Joseph W.; Bushley, Kathryn E.

doi:10.1186/s12864-018-5399-x

Cited by 24 publications

(18 citation statements)

References 96 publications

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“…The composite nature of gene clusters opens many evolutionary possibilities. Clusters might mutate, duplicate, divide into two, combine, or lose or gain new genes, occasionally through HGT (Fischbach et al ., ; Martín & Liras, ; Slot, ; Rokas et al ., ; Olarte et al ., ). Each of these possibilities is rife with methodological complications for evolutionary studies (Bull et al ., ; Castresana, ; Fischbach et al ., ).…”

Section: Metabolic Complexitymentioning

confidence: 97%

Fungal evolution: cellular, genomic and metabolic complexity

Naranjo‐Ortiz

Gabaldón

2020

Biological Reviews

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The question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.

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Section: Metabolic Complexitymentioning

confidence: 97%

Fungal evolution: cellular, genomic and metabolic complexity

Naranjo‐Ortiz

Gabaldón

2020

Biological Reviews

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“…Several ascomycetes, especially those in the Saccharomycotina, including the common baker's yeast Saccharomyces cerevisiae have known ancestral genome duplication events. Chromosomal translocation or the uncommon rearrangement of chromosomes also influences the incongruence in phylogeny, and it may occur more regularly in fungal genomes than earlier noticed (Olarte et al 2019). For instance, different strains of the entomopathogenic fungus Tolypocladium inflatum exhibit high diversity in production of cyclosporin and other secondary metabolites (Olarte et al 2019).…”

Section: Limitations Of Pscmentioning

confidence: 99%

Integrative approaches for species delimitation in Ascomycota

et al. 2021

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Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta (Dothideomycetes, Botryosphaeriales). Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.

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“…In particular, the maintenance of separate Cox–Bramley and Cox–Worcester groupings in the Cox V. inaequalis population could be explained by chromosomal rearrangements, with the loci conferring virulence lying within an inverted or translocated region; this would give rise to lethal recombinants in crosses heterogeneous for the rearranged regions. The proportion of the genome involved in, or affected by, rearrangements would be extensive but not unprecedented (Raeside et al , ; Shi‐Kunne et al , ; Olarte et al , ). As pointed out above, such chromosomal rearrangements would, of course, also be another explanation for the aggregation of GSAs.…”

Section: Discussionmentioning

confidence: 99%

Genomic sequencing indicates non‐random mating ofVenturia inaequalisin a mixed cultivar orchard

Passey

Armitage²,

Sobczyk³

et al. 2020

Plant Pathology

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Apple scab is one of the most economically important diseases of apples worldwide. The disease is caused by the haploid ascomycete Venturia inaequalis. Growing apples in cultivar mixtures may reduce disease severity. To determine how the pathogen population structure is affected by host mixtures we studied 24 V. inaequalis isolates sampled from three different apple cultivars (Bramley, Cox, and Worcester) growing in a mixed orchard approximately 50 years old. The isolates were aligned against a reference genome and single nucleotide polymorphisms (SNPs) were called between the isolates. The populations isolated from Bramley and Worcester were distinct, while Cox isolates were an admixture. This supports previous tests of the ability of isolates to cross‐infect hosts, and molecular comparisons using simple sequence repeats (SSRs). Genotype‐specific allele (GSA) loci were not distributed randomly across contigs in proportion to contig length, but were clustered. Clustered GSA loci were observed in almost all contigs. This indicates population differentiation across the whole genome, presumably due to lack of crossing‐over events between Bramley and Worcester isolates. This lack is probably due to physical separation effects: sexual mating is more likely to take place and succeed between isolates from lesions on the same leaf than from contact between independently infected leaves in leaf litter on the orchard floor. This would especially be the case if sexual reproduction is initiated before leaf‐fall.

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Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Cited by 24 publications

References 96 publications

Fungal evolution: cellular, genomic and metabolic complexity

Fungal evolution: cellular, genomic and metabolic complexity

Integrative approaches for species delimitation in Ascomycota

Genomic sequencing indicates non‐random mating ofVenturia inaequalisin a mixed cultivar orchard

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