A chromosome-level phased Citrus sinensis genome facilitates understanding Huanglongbing tolerance mechanisms at the allelic level in an irradiation-induced mutant

Sweet orange (SWO) originated from introgressive hybridization of pummelo and mandarin resulting in a highly heterozygous genome. Here, we assembled a chromosome-level phased Valencia SWO (DVS) genome with ∼98.5% completeness, high accuracy (QV=50.6), and the highest annotation BUSCO completeness (99.2%) thus far in citrus. DVS harbors a high level of allelic variances and enables study of allelic somatic structural mutations and corresponding allelic expression alteration in two SWO mutants, one with high Huanglongbing tolerance (T19) and one more sensitive (T78). In T78, a large deletion on the pummelo-origin chr8 causes regional allelic expression absence. In T19, seven upregulated genes are located at one terminal of a translocated segment, including three genes related to heat shock protein (HSP) regulation. Furthermore, 68 of 133 HSPs are significantly upregulated in T19, which may be related to its enhanced HLB tolerance by preventing phloem necrosis. The DVS will advance allelic level studies in citrus.