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Article|03 Nov 2022|OPEN
A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance
Bo Wu1 ,† , Qibin Yu2 ,† , Zhanao Deng3 , Yongping Duan4 , Feng Luo1 , and Frederick G. Gmitter Jr.,2 ,
1School of Computing, Clemson University, 100 McAdams Hall, Clemson, SC 29643, USA
2Department of Horticultural Sciences, Citrus Research and Education Center, University of Florida, IFAS, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
3Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
4USDA-ARS, U.S. Horticultural Research Laboratory, 2001 South Rock Road, Fort Pierce, FL 34945, USA
*Corresponding author. E-mail: luofeng@clemson.edu, fgmitter@uf l.edu
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhac247 (2023)
doi: https://doi.org/10.1093/hr/uhac247
Views: 486

Received: 18 Aug 2022
Accepted: 24 Oct 2022
Published online: 03 Nov 2022

Abstract

Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including CsDnaJCsHSP17.4B, and CsCEBPZ. Their upregulation is inferred to keep phloem protein homeostasis under the stress from HLB and enable subsequent stress responses observed in T19. DVS will advance allelic level studies in citrus.