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Journal article
Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance
The plant genome, Vol.19(2), e70232
2026
PMID: 41894487
Abstract
The genus Citrus is characterized by a reticulate evolutionary history with frequent hybridization, making it an intriguing subject for genome evolution investigation. Citrus changshan-huyou Y. B. Chang (Huyou) is a unique landrace first discovered in Zhejiang Province, China, with premium fruit quality. The evolutionary origin of Huyou has puzzled local botanists and growers. Here, we sequenced a 120-year-old "ancestral tree" of Huyou using PacBio long read and Hi-C sequencing and assembled two high-quality, haplotype-resolved genomes, HY1 and HY2. Huyou displayed a genome heterozygosity level at 3.07%, among the highest in published citrus genomes. Using a k-mer-based tracing approach, we explicitly resolved that HY1 genome contained 87.8% mandarin, 7.3% pummelo, and 0.2% citron origin, whereas HY2 had 85.0% pummelo, 2.9% mandarin, and 0.3% citron, implying a hybridization event between mandarin and pummelo. Phylogeny dating showed that HY1 (2.0 Mya) and HY2 (2.18 Mya) had diverged earlier than the split of Citrus clementina and Citrus reticulata and the split of Citrus grandis and Citrus maxima, respectively. We observed clear chromosomal recombination on chr8 and chr9 in HY1, which may have occurred after the ancestral hybridization. Further transcriptome analyses in six tissues revealed a strong allelic dominance of HY2 over HY1 in root tissue and moderately in stem, leaf, flower, and fruit. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed that genes related to antioxidant biosynthesis and lipid metabolism were most significantly affected by allelic imbalance. This pioneering report of allelic imbalance in citrus species support Huyou as an interesting model to investigate genome evolution following distant hybridization.
Details
- Title
- Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance
- Authors/Creators
- Zhanghui Zeng - Hangzhou Normal UniversityYingjie Luo - Hangzhou Normal UniversityHaifei Hu - Rice Research InstituteLan Lan - Murdoch UniversityBaojin Guo - Murdoch UniversityPing Zhou - BGI Group (China)Cong Tan - BGI Group (China)Xiaoping Huang - Hangzhou Normal UniversityTuo Qi - Mianyang Normal UniversityZhehao Chen - Hangzhou Normal UniversityZhiming Yu - Hangzhou Normal UniversityLilin Wang - Hangzhou Normal UniversityTaihe Xiang - Hangzhou Normal UniversityChengdao Li - Murdoch University, Centre for Crop and Food InnovationYong Jia - Murdoch University, School of Agricultural Sciences
- Publication Details
- The plant genome, Vol.19(2), e70232
- Publisher
- Wiley Periodicals LLC on behalf of Crop Science Society of America.
- Number of pages
- 22
- Grant note
- LQ23C130003 / Natural Science Foundation of Zhejiang Province 32301872 / National Natural Science Foundation of China; National Natural Science Foundation of China (NSFC) 2025JCXK01 / Interdisciplinary Research Project of Hangzhou Normal University
- Identifiers
- 991005876850207891
- Copyright
- © 2026 The Author(s).
- Murdoch Affiliation
- Centre for Crop and Food Innovation; School of Agricultural Sciences; State Agricultural Biotechnology Centre
- Language
- English
- Resource Type
- Journal article
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