Zezhen Du
Postdoctoral AssociateAbout
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Featured Publications
A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Du Z, He J, Jiao W. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25: 91. PMID: 38589937, PMCID: PMC11003132, DOI: 10.1186/s13059-024-03239-1.Peer-Reviewed Original ResearchConceptsPlant genomesGenotyping methodsComplexity of plant genomesHeterozygous plant genomesGenotypic algorithmsGenotype millionsShort readsGenomic contextGenomic diversitySequencing technologiesHuman genomeGenomeGenetic variantsExcessive repeatsVariant typeGenotypesStructural variationsEnsemble pipelinePlantsConclusionsOur studyVariant genotypesGenotype performanceVariantsDeletionSequenceSynDiv: An efficient tool for chromosome collinearity-based population genomics analyses
Du Z, He J, Jiao W. SynDiv: An efficient tool for chromosome collinearity-based population genomics analyses. Plant Communications 2024, 5: 101071. PMID: 39182168, PMCID: PMC11671753, DOI: 10.1016/j.xplc.2024.101071.Peer-Reviewed Original ResearchCharacterization of the PHOSPHATE RESPONSE 2-dependent and -independent Pi-starvation response secretome in rice
Du Z, Deng S, Wu Z, Cai H, Xu F, Shi L, Wang S, Ding G, Wang C. Characterization of the PHOSPHATE RESPONSE 2-dependent and -independent Pi-starvation response secretome in rice. Journal Of Experimental Botany 2022, 73: 6955-6970. PMID: 35994773, DOI: 10.1093/jxb/erac342.Peer-Reviewed Original ResearchConceptsCell wall remodeling proteinsSuspension-cultured cellsSignal transduction proteinsPi signaling pathwayReactive oxygen speciesTransduction proteinsWild-typePathogen-relatedDifferentially expressed secreted proteinsSignaling pathwayPi-deficient conditionsPi-responsive genesCell wall compositionRegulating stress responsesCell wall structurePi-starvationPi-sufficientPi-repletePathogen resistancePlant cellsReactive oxygen species contentMetabolic proteinsSecreted proteinsPR proteinsTranscription factorsGenome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice
Du Z, Deng S, Wu Z, Wang C. Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice. PLOS ONE 2021, 16: e0245600. PMID: 33481906, PMCID: PMC7822558, DOI: 10.1371/journal.pone.0245600.Peer-Reviewed Original ResearchConceptsHAD genesHAD proteinsHAD superfamilyStarvation responseMining of transcriptome dataPi starvation responsesGenome-wide analysisPhosphate starvation responsePi stress conditionsHaloacid dehalogenase geneGenes of riceSequence similarityGenome searchPhosphatase domainPi starvationCap domainCis-elementsMotif analysisQRT-PCR resultsTranscriptome dataDehalogenase genesCollinear relationshipsBioinformatics analysisGenesOrganic phosphate substratesVarigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes
Du Z, He J, Xiao P, Hu J, Yang N, Jiao W. Varigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes. Molecular Plant 2025, 18: 1587-1601. PMID: 40770875, DOI: 10.1016/j.molp.2025.08.001.Peer-Reviewed Original ResearchConceptsPangenome graphsGenomics-assisted breedingPolyploid genomesPlant genomesHuman genomeRepetitive k-mersPlant genome studiesNon-human genomesGraph-based genotypingVariant genotypesPangenome referenceShort readsRepetitive regionsVariant sitesRice genomeK-mersPopulation geneticsGenomic studiesQuantitative geneticsGenotyping methodsGenomeAllele dosagePangenomeDownstream applicationsGenotypes
2025
Pan-S-locus analysis reveals insights into the origin and evolution of self-incompatibility in the orange subfamily
Hu J, Du Z, Liu C, Wen H, Liu C, Chen P, Shi C, Ye J, Ji Q, Deng X, Bosch M, Lin Z, Jiao W, Chai L. Pan-S-locus analysis reveals insights into the origin and evolution of self-incompatibility in the orange subfamily. Genome Biology 2025, 26: 344. PMID: 41057937, PMCID: PMC12506349, DOI: 10.1186/s13059-025-03817-x.Peer-Reviewed Original ResearchConceptsOrange subfamilyEvolution of self-incompatibilitySelf-incompatibility systemSelf-incompatibilityS-locusS-RNaseGametophytic self-incompatibility systemSelf-compatible populationsSelf-incompatibility mechanismGenotyping pipelineSLF genesCitrus genomeRepetitive sequencesEvolutionary trajectoriesSupergene complexEvolutionary mechanismsEvolutionary dynamicsSubfamilyPlant familiesBackgroundSelf-incompatibilityStructural diversificationGenomePrimary driverStructural variationsComprehensive libraryPlant graph-based pangenomics: techniques, applications, and challenges
Du Z, He J, Jiao W. Plant graph-based pangenomics: techniques, applications, and challenges. ABIOTECH 2025, 6: 361-376. PMID: 40641648, PMCID: PMC12237840, DOI: 10.1007/s42994-025-00206-7.Peer-Reviewed Original ResearchNovo-assembled genomeMolecular breeding of cropsDNA sequencing technologiesInvestigate population diversityAgronomically important genesBreeding of cropsPangenome graphsGenetic mapSmall variantsGenomic regionsGenetic diversityGraph pangenomeSequencing technologiesGenomic analysisPangenomic studiesGenomic studiesGenetic variationImportant genesMolecular breedingStructural variantsPangenomeGenomeCrop breedingPlantsVariantsSomatic variations in the meiosis‐specific gene CrMER3 confer seedlessness in a citrus bud sport
Fan Y, Du Z, He X, Liu Z, Zhuang J, Xiao G, Duan Y, Tan F, Xie K, Jiao W, Zhang F, Yang C, Guo W, Wu X. Somatic variations in the meiosis‐specific gene CrMER3 confer seedlessness in a citrus bud sport. Journal Of Integrative Plant Biology 2025, 67: 1649-1664. PMID: 39981730, DOI: 10.1111/jipb.13872.Peer-Reviewed Original ResearchConceptsKompetitive allele-specific PCRFruit cropsSeedless cultivarsSeedless hybridsSeedless varietiesFresh consumptionBud sportsCitrus germplasmSeed abortionSeedlessCultivarsWild mandarinAllele-specific PCRCitrusCropFruitBreedingNatural variationNatural mutationsSterilizationCultivated mandarinsMandarinMeiosis defectsGermplasmMeiotic prophase I
2024
A rare inter-haplotypic recombination at the S-locus contributed to the loss of self-incompatibility in trifoliate orange
Hu J, Guo F, Du Z, Chen P, Shi C, Zhang J, Ye J, Deng X, Larkin R, Jiao W, Lin Z, Bosch M, Chai L. A rare inter-haplotypic recombination at the S-locus contributed to the loss of self-incompatibility in trifoliate orange. Plant Communications 2024, 5: 100940. PMID: 38715365, PMCID: PMC11412923, DOI: 10.1016/j.xplc.2024.100940.Peer-Reviewed Original Research
2023
Transposable elements cause the loss of self‐incompatibility in citrus
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin R, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong V, Chai L. Transposable elements cause the loss of self‐incompatibility in citrus. Plant Biotechnology Journal 2023, 22: 1113-1131. PMID: 38038155, PMCID: PMC11022811, DOI: 10.1111/pbi.14250.Peer-Reviewed Original ResearchConceptsMiniature inverted-repeat transposable elementsMiniature inverted-repeat transposable element insertionSelf-incompatibilityTransposable elementsS-locusS-RNaseS-RNase-based SI systemPromoter regionLoss of self-incompatibilityPromote genetic diversityS-RNase allelesPrezygotic mechanismsGenetic diversityInbreeding depressionSelf-compatibleNucleotide mutationsFlowering plantsLoss of SiTransgenic experimentsBreeding strategiesCitrus genusAllelesSI phenotypePromoterCitrus
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