Improvements in the Tomato Reference Genome (SL3.0) and Annotation (ITAG3.0)

The Solanum lycopersicum cultivar Heinz 1706 genome is the primary reference model organism for many solanaceous species. Here we are describing our efforts to improve reference genome and annotation of tomato. 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. BioNano optical maps generated for heinz 1706 largely confirmed reference genome assembly with few rearrangements resulting in the SL3.0 genome build.

We also present an improved annotation (ITAG 3.0) for the new tomato reference genome. The annotation pipeline involved updating ITAG2.40 gene models, preserving locus identifiers (solyc ids) from the previous ITAG2.40 annotation and identifying new gene models using newly trained ab-initio gene predictors. We have incorporated expression data from various sources in our pipeline including tissue and treatment specific RNAseq data, 5’ and 3’ UTR enriched RNA sequencing, RENseq for NBS-LRR genes and Pacbio Iso-seq RNA data which were all kindly provided by Solanaceae community. More than 8 billion Illumina RNAseq reads were mapped to the SL3.0 genome with more than 85% mapping rate. The de novoprediction of genes in the maker pipeline has identified more than 2500 novel genes well-supported by expression evidence that are not present in ITAG2.40. The increased continuity of the genome in SL3.0 and availability of diverse and comprehensive expression data resulted in a significantly improved tomato annotation (ITAG3.0).

All data are available through the SOL Genomics Network website (SGN, https://solgenomics.net) and FTP site (ftp://ftp.solgenomics.net/tomato_genome/).