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Article|14 Feb 2023|OPEN
A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance
Yixue Bao1,2 ,† , Ziyan Zeng1,3 ,† , Wei Yao1 , Xiao Chen3 , Mengwei Jiang3 , Akbar Sehrish1 , Bo Wu4 , Charles A. Powell5 , Baoshan Chen1 and Jianlong Xu2 , Xingtan Zhang1,3 , , Muqing Zhang,1,5 ,
1State Key Laboratory for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning 530005, China
2Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
4School of Computing, Clemson University, 821 McMillan Rd, Clemson, SC 29631, USA
5IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA
*Corresponding author. E-mail:,mqzhang@uf
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad020 (2023)
Views: 43

Received: 03 Aug 2022
Accepted: 06 Feb 2023
Published online: 14 Feb 2023


The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruits worldwide. Lemon also tolerates huanglongbing (HLB) disease, which is a devastating citrus disease. Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps, while a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5%), 147.4 Mb from mandarin (23.3%), and 147.1 Mb from pummelo (23.2%). The genome included 30 528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant–pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor compounds. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.