PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza

Modern commercial varieties of tomato (Solanum lycopersicum) are typically F1 hybrids that are genetically heterozygous. Here we generated haplotype-aware assemblies of two different tomato commercial hybrids (Funtelle and Maxeza) using PacBio HiFi reads. The HiFi data was assembled using the Hifiasm assembler allowing for the generation of contigs that distinguish the two parental haplotypes (haplotype-aware assembly). Reference based scaffolding was used to generate the chromosome-scale assemblies available here. It should be noted that although the raw assembly manages to fully distinguish haplotypes we did not test whether the working reference sequence we make available here is fully phased at the chromosome level. Methods The raw PacBio HiFi sequencing reads of the both varieties studied here are available via the European Nucleotide Archive under project numbers PRJEB62442 (Funtelle) and PRJEB62443 (Maxeza). For scientific correspondence please contact Charles Underwood (cunderwood[@]mpipz.mpg.de)