Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia
Fig 5
Nucleotide identity (%) between tetraploid iuLoeVari1. µ haplotypes.
Each haplotype was compared to the other three haplotypes using minimap2 [95], and nucleotide identity (%) between them was plotted for each reference. Each haplotype has a mosaic pattern of identity to the others. The gray shaded area represents a “missing” segment of chromosome 1D, which we suggest is identical to and thus coassembled as the corresponding portion of chromosome 1C, which has double the expected coverage. The top panel of each plot shows mapped read coverage, and the middle panel displays GC content along the chromosome, with average GC content marked by a dashed red line. The coverage data underlying this figure was generated by mapping the PacBio reads against the genome using minimap2, and extracting read depth data using samtools and bedtools [96,97]. The GC data was generated by running seqkit fx2tab [98] on the genome. The genome can be found in File Collection 12 at https://doi.org/10.5281/zenodo.17251512. The genome’s BioSpecimenID can be found in S1 Table, and can be used to retrieve the associated PacBio reads from NCBI [99]. The figure was generated using Matplotlib [92], and manually annotated using InkScape (version 1.2.2).