‘Hamlin 1-4-1’ sweet orange (Citrus sinensis L. Osbeck) is one of the major varieties cultivated in Florida and is of relevant importance for the orange juice industry as an early maturing variety. While this cultivar does not produce juice of sufficient quality to meet USDA Grade A orange juice standards, it performs relatively well in semitropical climates characterized by high temperatures and humidity levels. To provide the bioinformatics tools required to support the genetic improvement of modern citrus varieties, we present the de novo and fully phased ‘Hamlin’ genome. The DNA of the plant was sequenced using two different platforms. PacBio technology was adopted to generate long reads sequencing, while Oxford Nanopore was employed to produce ultra-long reads. Hi-C technique was used to capture chromosome conformation and facilitate the correct assembly of contigs into two haplotypes. RNA samples were collected from five different tissues (leaves, petals, ovaries, peel, and bark) and sequenced with the Illumina platform. These RNA sequences enabled the identification and annotation of as many functional genes as possible. The results of this study will provide the genomic information required to compare the ‘Hamlin 1-4-1 genome with the more commonly grown industry standard ‘Valencia’ and to investigate the differences between the genomes of these two clonally derived sweet oranges. These data will also aid in comparing budlines of Hamlin and other sweet orange accessions that appear to be HLB tolerant. This research will facilitate the detection of DNA variants related to traits of interest and their integration in new germplasm resources. In addition, it will allow breeders to get further insights into mutations that may have occurred to new budlines originating from ‘Hamlin’.
