Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres

In this study, we have constructed a gapless and chromosome-level genome assembly of Candida tropicalis type strain MYA-3404 using PacBio long reads, simplified Hi-C (3C-seq) data and the previously available contigs in three steps. First, the contigs from reference genome assembly were scaffolded using NGS data into 16 contigs. Next, a SMIS run using the PacBio reads produced an assembly in 12 contigs. Thirdly, we used 3C-seq data, genetic analysis and chromoblot analysis to prove five small contigs as heterozygous regions in the diploid genome of C. tropicalis strain MYA-3404, and subsequently validated the genome assembly in seven chromosomes. Next, we explored the 3D chromatin organization of C. tropicalis genome using high-throughput 3C-seq data. We have also performed Oxford Nanopore and Illumina sequencing to generate a contig-level de novo genome assembly of Candida sojae strain NCYC-2607.