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Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

Fig 3

Identification and characterization of centromeres on each of the 14 chromosomes in the CBS6039 genome.

(A) Live cell direct fluorescence microscopy images of centromere binding protein Cse4 (CENP-A) at 3 different stages of the mitotic cycle. (B) Plots of read depths when mCherry-CENP-A chromatin immunoprecipitation sequencing (ChIP-seq) data were mapped against the CBS6039 genome assembly are presented. All of the centromeric regions identified in the CBS6039 genome (except for chromosome 1; see Results for more details) showed significantly higher read depth when compared to flanking non-centromeric regions (see S3 Fig for plots of whole chromosomes). Red plots (chipD) are based on signals obtained from ChIP-seq analysis, while blue plots (contD) indicate the negative control. (C) The diagram depicts the structures of the 6 unique centromere-specific Long Terminal Repeat (LTR) retrotransposons, Tcen (transposons in centromeres) 1–6, identified in the Cryptococcus amylolentus centromeric regions. While Tcen1 contains only LTRs (shown in grey), all of the other 5 Tcen elements consist of various genes/domains found in retrotransposons (RH, RNaseH; RT, Reverse Transcriptase; INT, Integrase). On the far right are the corresponding centromeres in the CBS6039 genome within which the full-length Tcen elements have been identified. (D) Schematic illustrating the distributions of the 6 Tcen elements, as well as their remnants, on the identified centromere regions in the CBS6039 genome. These intervals were defined as the longest ORF-free regions on the respective chromosomes and contain mostly retrotransposons or their remnants, and show enrichment of CENP-A binding based on ChIP-seq analyses. (E) RNA sequencing (RNA-seq) analysis reveals that the identified CBS6039 centromere regions also had reduced levels of transcriptional activity when compared to flanking non-centromeric regions. The blue bars indicate RNA-seq read depth. Please see S3 Table for coordinates of the centromeres in C. amylolentus.

Fig 3