Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements

Svedberg, Jesper; Hosseini, Sara; Chen, Jun; Vogan, Aaron A.; Mozgová, Iva; Hennig, Lars; Manitchotpisit, Pennapa; Abusharekh, Anna; Hammond, Thomas M.; Lascoux, Martin; Johannesson, Hanna

doi:10.1038/s41467-018-06562-x

Cited by 49 publications

(65 citation statements)

References 76 publications

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“…The cortex gene is trapped within the inversion and has been implicated in color patterning across Heliconius and other Lepidoptera, but there is no clear phenotype that unites erato-sara clade species having this inversion. Nonetheless, due to the known effects of cortex and the fact that convergent structural rearrangements have been found rarely and in important contexts such as mating loci and meiotic drive loci in fungi 57,58 , and as a basis for social organization in ants 59 , this locus should be the object of further study.…”

Section: Discussionmentioning

confidence: 99%

Genomic architecture and introgression shape a butterfly radiation

Edelman

Frandsen

Miyagi

et al. 2018

Preprint

129

216

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We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

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Section: Discussionmentioning

confidence: 99%

Genomic architecture and introgression shape a butterfly radiation

Edelman

Frandsen

Miyagi

et al. 2018

Preprint

129

216

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“…We sequenced the N. sitophila genomes on the PacBio RSII platform (Pacific Biosciences) at Uppsala Genome Centre (SciLifeLab, Uppsala, Sweden) using four SMRT cells per sample and the C4 chemistry and P6 polymerase (Pacific Biosciences). The strains were prepared as in Svedberg et al [71]. Raw PacBio sequence data were filtered and assembled using the SMRT Analysis package and HGAP 3.0 assembler (Pacific Biosciences, https://github.com/ PacificBiosciences/).…”

Section: Genomic Resourcesmentioning

confidence: 99%

Comparative analysis of genome-wide DNA methylation in Neurospora

et al. 2020

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DNA methylation is an epigenetic mark that plays an important role in genetic regulation in eukaryotes. Major progress has been made in dissecting the molecular pathways that regulate DNA methylation. Yet, little is known about DNA methylation variation over evolutionary time. Here we present an investigation of the variation of DNA methylation and transposable element (TE) content in species of the filamentous ascomycetes Neurospora. We generated genome-wide DNA methylation data at single-base resolution, together with genomic TE content and gene expression data, of 10 individuals representing five closely related Neurospora species. We found that the methylation levels were low (ranging from 1.3% to 2.5%) and varied among the genomes in a species-specific way. Furthermore, we found that the TEs over 400 bp long were targeted by DNA methylation, and in all genomes, high methylation correlated with low GC, confirming a conserved link between DNA methylation and Repeat Induced Point (RIP) mutations in this group of fungi. Both TE content and DNA methylation pattern showed phylogenetic signal, and the species with the highest TE load (N. crassa) also exhibited the highest methylation level per TE. Our results suggest that DNA methylation is an evolvable trait and indicate that the genomes of Neurospora are shaped by an evolutionary arms race between TEs and host defence.

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“…Because early hyphae were uncompartmentarized, their evolution could have bypassed the need to resolve group conflicts and align the fitness of individual cells 7 . Alternatively, it is possible that conflicts are resolved at the level of individual nuclei 20 . Second, hyphae maximize foraging and nutrient assimilation efficiency and minimize competition for nutrients by a fractal-like growth mode 16,21,22 .…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics reveals the origin of fungal hyphae and multicellularity

Kiss

Hegedis

Varga

et al. 2019

Preprint

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65Hyphae might have also facilitated the transition of fungi to terrestrial life 23 and confer immense 66 medical relevance to pathogenic fungi 24 . Hyphae of extant fungi rarely stick to each other in 67 vegetative mycelia and adhesion becomes key only in fruiting bodies 25-27 -which, in terms of 68 complexity level, resemble complex multicellular metazoans and plants 7,28 -or in the attachment 69 to host surfaces 29 . Thus, whereas in most multicellular lineages adhesion, cell-cell cooperation, 70communication and differentiation represent the main hurdles to the emergence of multicellular 71 precursors 3,6,30-32 , fungi might have had different obstacles to overcome. 72 73While the origins of hyphae are poorly known, information on the molecular and cellular 74 basis of hyphal morphogenesis is abundant (for recent reviews see refs [33][34][35][36][37][38] ), permitting 75 evolutionary genomic analyses of the origins of hyphae. Hyphal morphogenesis builds on cell 76 polarization networks 39 , the exo-and endocytotic machinery 40 , long range vesicle transport as 77 well as fungal-specific traits such as cell wall synthesis and assembly 41 , and the selection of 78 branching points and sites of septation 42 , among others. A key structure of hyphal growth is the 79Spitzenkörper 43 , which acts as a distribution center for vesicles transporting cell wall materials 80and various factors to the hyphal tip. The cytoplasmic microtubule network provides the 81 connection between vesicle cargo through the ER and Golgi and the Spitzenkörper, from where 82

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Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements

Cited by 49 publications

References 76 publications

Genomic architecture and introgression shape a butterfly radiation

Genomic architecture and introgression shape a butterfly radiation

Comparative analysis of genome-wide DNA methylation in Neurospora

Comparative genomics reveals the origin of fungal hyphae and multicellularity

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