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

Fuentes, Roven Rommel1; van Rengs, Willem M. J.1; Wang, Yazhong1; Underwood, Charles1

Published Oct 12, 2023 on Dryad. https://doi.org/10.5061/dryad.931zcrjs4

Data files

Oct 12, 2023 version files 3.43 GB

Abstract

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.