P0798Improved Tomato Genome Reference (SL3.0) using Full-Length BACs, BioNano Optical Maps and SGN Community Resources
Improved Tomato Genome Reference (SL3.0) using Full-Length BACs, BioNano Optical Maps and SGN Community Resources
The Solanum lycopersicum cultivar Heinz 1706 genome is the primary reference model organism for many solanaceous species. The previous genome build SL2.50 contained 23,640 contig gaps and 79 scaffold gaps where the size was an approximation and the bases were unknown. The total size of gap regions varied from 7.23% to 14.61% per chromosome and was 10.36% for the entire genome.
We have integrated 1,069 full-length phase htgs3 BACs into the tomato genome to cover gap regions and replace shorter whole genome shotgun contigs which removed 11,699,806 bases (11Mb) of contig gaps. The reduction in contig gaps varied from 3.17% to 49.07% per chromosome. BioNano genome maps were generated for Heinz 1706 that largely confirmed the correctness of the current build. Chromosome 0 contains scaffolds that could not be localized in the genome build. In the new SL3.0 build, we were able to integrate 2 additional scaffolds from chromosome 0 into chromosomes 2 and 9, fix 2 inversions in chromosome 12 and resize 19 gaps accurately using CMaps from the assembly of BioNano optical maps.
All data are available through the SOL Genomics Network website (SGN, https://solgenomics.net) and FTP site (ftp://ftp.solgenomics.net/tomato_genome/).