Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance

Citrus is an interesting model for plant genome evolution study due to its reticulate evolutionary history with frequent hybridization. Citrus changshan 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. Here, we sequenced a 120-years-old “ancestral tree” of Huyou and assembled two haplotype-resolved genomes HY1 and HY2. Huyou displayed 3.07% genome heterozygosity level, the highest in published citrus genomes. K-mer-based genome tracing revealed that HY1 contained 87.8% mandarin, 7.3% pummelo, 0.2% citron origin, whereas HY2 had 85.0% pummelo, 2.9% mandarin, 0.3% citron, implying a clear hybridization origin. Phylogeny dating showed that HY1 (2.0Mya) and HY2 (2.18Mya) had diverged earlier than the split of Citrus clementina and Citrus reticulata , and the split of Citrus grandis and Citrus maxima , respectively. Further transcriptome analyses revealed a strong allelic dominance of HY2 over HY1 in root tissue and moderately in stem, leaf, flower, and fruits. We found that genes related to antioxidants biosynthesis and lipid metabolisms were most significantly affected by allelic imbalance. This first report of allelic imbalance in citrus species support Huyou as an interesting model to investigate genome evolution following distant hybridization.