Centromere evolution in the fungal genusVerticillium

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>Centromeres are chromosomal regions that are crucial for chromosome segregation during mitosis and meiosis, and failed centromere formation can contribute to chromosomal anomalies. Despite this conserved function, centromeres differ significantly between and even within species. Thus far, systematic studies into the organization and evolution of fungal centromeres remain scarce. In this study, we identified the centromeres in each of the ten species of the fungal genus <jats:italic>Verticillium</jats:italic> and characterized their organization and evolution. Chromatin immunoprecipitation of the centromere-specific histone CenH3 (ChIP-seq) and chromatin conformation capture (Hi-C) followed by high-throughput sequencing identified eight conserved, large (∼150 kb), AT-, and repeat-rich regional centromeres that are embedded in heterochromatin in the plant pathogen <jats:italic>V. dahliae</jats:italic>. Using Hi-C, we similarly identified repeat-rich centromeres in the other <jats:italic>Verticillium</jats:italic> species. Strikingly, a single repetitive element is strongly associated with centromeric regions in some but not all <jats:italic>Verticillium</jats:italic> species. Extensive chromosomal rearrangements occurred during <jats:italic>Verticillium</jats:italic> evolution, yet only a minority could be linked to centromeres, suggesting that centromeres played a minor role in chromosomal evolution. Nevertheless, the size and organization of centromeres differ considerably between species, and centromere size was found to correlate with the genome-wide repeat content. Overall, our study highlights the contribution of repetitive elements to the diversity and rapid evolution of centromeres within the fungal genus <jats:italic>Verticillium</jats:italic>.</jats:p><jats:sec><jats:title>IMPORTANCE</jats:title><jats:p>The genus <jats:italic>Verticillium</jats:italic> contains ten species of plant-associated fungi, some of which are notorious pathogens. <jats:italic>Verticillium</jats:italic> species evolved by frequent chromosomal rearrangements that contribute to genome plasticity. Centromeres are instrumental for separation of chromosomes during mitosis and meiosis, and failed centromere functionality can lead to chromosomal anomalies. Here, we used a combination of experimental techniques to identify and characterize centromeres in each of the <jats:italic>Verticillium</jats:italic> species. Intriguingly, we could strongly associate a single repetitive element to the centromeres of some of the <jats:italic>Verticillium</jats:italic> species. The presence of this element in the centromeres coincides with increased centromere sizes and genome-wide repeat expansions. Collectively, our findings signify a role of repetitive elements in the function, organization and rapid evolution of centromeres in a set of closely related fungal species.</jats:p></jats:sec>

DNA methylation inVerticillium dahliaerequires only one of three putative DNA methyltransferases, yet is dispensable for growth, development and virulence

“…We recently reported that wild-type V. dahliae displays relatively low levels of DNA methylation, with an average of ∼0.4% methylation in CG and CHG context and essentially no DNA methylation in CHH context (Cook et al ., 2020). DNA methylation in V. dahliae is restricted to particular inactive transposons that locate in condensed, H3K9me3-enriched, chromatin regions in the core genome, including those localized in centromeres (Figure 3A) (Cook et al ., 2020; Seidl et al ., 2020). We furthermore showed that the Δ Hp1 mutant lost all DNA methylation, indicating that Hp1 is required for cytosine methylation and V. dahliae DNMTs cannot methylate DNA independently (Cook et al ., 2020).…”

“…Sexual reproduction has not been reported for V. dahliae that is presumed to mainly reproduce asexually (de Jonge et al ., 2013). Recently, we demonstrated that DNA methylation in V. dahliae requires Hp1 and is restricted to H3K9me3-enriched transposons that localize mainly in evolutionary stable core genomic regions that are typically shared across different V. dahliae strains, including centromere regions (Cook et al ., 2020; Seidl et al ., 2020). In contrast to stable core regions, genomic regions that are important for adaptation show extensive presence-absence polymorphisms between V. dahliae strains, and are therefore designated as lineage-specific (LS) (Klosterman et al ., 2011; de Jonge et al ., 2013; Faino et al ., 2016; Depotter et al ., 2019; Cook et al ., 2020).…”

DNA methylation in Verticillium dahliae requires only one of three putative DNA methyltransferases, yet is dispensable for growth, development and virulence

“…Sexual reproduction has not been reported for V. dahliae that is presumed to mainly reproduce asexually (de Jonge et al, 2013). Recently, we demonstrated that DNA methylation in V. dahliae requires Hp1 and is restricted to H3K9me3-enriched transposons that localize mainly in evolutionary stable core genomic regions that are typically shared across different V. dahliae strains, including centromere regions (Cook et al, 2020;Seidl et al, 2020). In contrast to stable core regions, genomic regions that are important for adaptation show extensive presenceabsence polymorphisms between V. dahliae strains, and are therefore designated as lineagespecific (LS) (Klosterman et al, 2011;de Jonge et al, 2013;Faino et al, 2016;Depotter et al, 2019;Cook et al, 2020).…”

“…We recently reported that wild-type V. dahliae displays relatively low levels of DNA methylation, with an average of ~0.4% methylation in CG and CHG context and essentially no DNA methylation in CHH context (Cook et al, 2020). DNA methylation in V. dahliae is restricted to particular inactive transposons that locate in condensed, H3K9me3-enriched, chromatin regions in the core genome, including those localized in centromeres ( Figure 3A) (Cook et al, 2020;Seidl et al, 2020). We furthermore showed that the ∆Hp1 mutant lost all DNA methylation, indicating that Hp1 is required for cytosine methylation and V. dahliae DNMTs cannot methylate DNA independently (Cook et al, 2020).…”