Telomere-to-Telomere Chromosome Assemblies and Identification of Structural Variations in Arabidopsis thaliana Ecotypes

Individual genomes harbor structural variations, such as insertions and deletions ranging from several hundred to millions of base pairs. Although most identified variations have biological impact and are of evolutionary significance, technical limitations have not allowed the study of SVs on the whole-genome or population level until recently.

Here we report the utilization of the BioNano Genomics Irys platform to create physical genome maps for 10 diverse Arabidopsis thaliana ecotypes. We identified over 300 SVs per ecotype between 2 kb to 1.2 Mb, if compared to the reference Col-0. Sites and types of SVs are similar between all ecotypes, mainly around the centromere, and evolutionary hotspots like NLR-type disease resistance gene clusters.

The combination of physical Irys maps and PacBio SMRT sequencing allowed the hybrid assembly of all five chromosomes of A. thaliana ecotype Landsberg erecta (Ler-0) into single contigs. The Ler-0 genome size is 123 Mb, excluding rRNA and Telomere caps at chromosomes 2 and 4. Irys maps were used to order PacBio scaffolds around the centromere, and the gained sequence information provides unprecedented insights of the centromeric structure, size and repeat vs. non-repeat content. RNAseq data was further used to identify the centromere specific transcriptome.