Chromosome-level diploid genome assembly of apomictic Boechera hybrid M4B

The purpose of the project was to produce a genome assembly suitable to study the origin, evolution and mechanisms of apomixis in Boechera genus. Boechera hybrid M4B, apomict which have aneuploid diploid cytotype with 2n = 15 was used for sequencing. We specifically aimed to obtain assembly with fully resolved homologous (diploid) chromosomes to preserve true structure of apomictic genome which facilitates discovery of apomixis related genomic regions. To produce the assembly long read sequencing data (ONT) was assembled by Canu assembler. Resulted assembly was corrected by Nextpolish pipeline using short reads sequencing data (Illumina). Polished assembly was scaffolded by Bionano Genomics pipeline and optical mapping data. Resulted super-scaffolds were assigned to chromosomes based on GISH experiments.