The genomic data of Newhall (Citrus sinensis [L.] Osb. cv. Newhall)

Sweet orange (<i>Citrus sinensis</i><em> </em>Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its susceptibility to low-temperature stress limits its cultivation and production in regions prone to frost damage, severely impacting the sustainable development of the sweet orange industry. Therefore, developing cold-resistant sweet orange varieties is of great necessity. Traditional hybrid breeding methods are not feasible due to the polyembryonic phenomenon in sweet oranges, necessitating the enhancement of its germplasm through molecular breeding. High-quality reference genomes are valuable for studying crop resistance to biotic and abiotic stresses. However, the lack of genomic resources for cold-resistant sweet orange varieties has hindered the progress in developing such varieties and researching their molecular mechanisms of cold resistance. <br>This study integrated PacBio HiFi, ONT, Hi-C, and Illumina sequencing data to assemble telomere-to-telomere (T2T) reference genomes for the cold-resistant sweet orange wild-type counterpart Newhall (<i>Citrus sinensis</i> [L.] Osb. cv. Newhall). Comprehensive evaluations based on multiple criteria revealed that both genomes exhibit high continuity, completeness, and accuracy. The genome size was calculated as 346.33 Mb, with contig N50 36.77 Mb. In total 30,021 gene models were annotated in the genome. Leveraging the assembled genome, using comparative genomics analyses with another cultivar, we elucidated the evolutionary history of the sweet orange genome.