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., 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), , # PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza [https://doi.org/10.5061/dryad.931zcrjs4](https://doi.org/10.5061/dryad.931zcrjs4) Organism name: *Solanum lycopersicum* Cultivar name: Funtelle Assembly level: Reference-anchored contigs Assembler: hifiasm + RagTag Sequencing technology: PacBio HiFi European Nucleotide Archive project: PRJEB62442 Organism name: *Solanum lycopersicum* Cultivar name: Maxeza Assembly level: Reference-anchored contigs Assembler: hifiasm + RagTag Sequencing technology: PacBio HiFi European Nucleotide Archive project: PRJEB62443 MD5sum: Funtelle-1.fasta 87a62db087f03992c278fdd56dcd10d7 Funtelle-2.fasta 6c465e49d5072f4003477d0852ad7829 Maxeza-1.fasta 078a41440661f66be779ff6d2b721ff1 Maxeza-2.fasta 6e3100ec131cb8ccec932eea5e6f07ef Assembly Statistics: Funtelle1 Contigs 1,155 Total length (Mb) 875.2 Max length (Mb) 76.1 N50 length (Mb) 56.5 N90 length (Mb) 1.3 L50 7 L90 29 Funtelle2 Contigs 651 Total leng...