基本情况

焦文标，华中农业大学信息学院教授、博士生导师，果蔬园艺作物种质创新与利用全国重点实验室、湖北洪山实验室、农业生物信息湖北省重点实验室固定研究人员，先后获国家级、省级等人才项目资助。

       本课题组以马铃薯等作物为研究对象，利用高通量组学和AI技术，通过基因组学算法创新，解析作物驯化与重要性状形成的演化机制，挖掘并利用AI辅助设计共性调控元件，为基因组辅助园艺作物育种提供理论基础和技术支撑。本课题组主要研究成果发表在Nat. Genet., Nat. Communi., Genome Biol., Genome Res.等期刊上。      

       欢迎有生物信息学、生物学、计算机科学、统计学等相关学科背景的本科生、硕士/博士研究生、博士后等加入我们课题组。本课题组长年招聘博士后，欢迎邮件联系。

主要研究方向：

1. 基因组学算法开发与应用

   1) 基因组组装  针对杂合二倍体、同源多倍体等复杂基因组，开发单倍型与T2T组装算法。

   2) 泛基因组与变异鉴定分型 开发适用于杂合二倍体和多倍体作物的各类遗传变异鉴定与分型算法。

   3) 基因组进化 开发群体或进化基因组学算法，解析基因组进化机制、挖掘遗传变异的功能效应。

2. 园艺作物多组学大数据与智能设计育种 

   1) 马铃薯多组学与智能设计育种：通过组学算法的创新，如单倍型组装、变异识别与分型、多倍体GWAS & GS、多倍体基因组AI模型等，助力多倍体马铃薯种质资源基因型鉴定、功能基因挖掘、智能设计育种等。

   2) 园艺作物共性调控元件的挖掘与应用：整合进化生物学、高通量组学技术，挖掘园艺作物共性性状的调控元件和网络；开发深度学习模型，智能设计与优化调控元件。

   3) 园艺大数据平台构建与维护：通过与本室其他课题组的合作，构建园艺作物多组学大数据综合研究平台。

   
   

教育经历

•    2014.01-2017.06，德国马克斯普朗克植物育种研究所，生物信息学，博士

•    2014.01–2018.01，德国科隆大学（联合培养），生物信息学，博士

•    2010.09–2013.06，华中农业大学，生物化学与分子生物学，硕士

•    2006.09–2010.06，华中农业大学，生物学基地班，学士

工作经历

•    2021.04-至今，华中农业大学信息学院 教授

•    2021.01-2021.03 德国慕尼黑大学 博士后

•    2017.07-2020.12 德国马克斯普朗克植物育种研究所 博士后

科研项目

（1）华中农业大学高层次人才启动经费 在研 主持 （2021.4-2026.4）

（2）国家青年人才项目 在研 主持 （2023.1-2025.12）

（3）国家自然科学基金面上项目 在研 主持 （2023.1-2026.12）

（4）武汉英才优秀青年人才 在研 主持 （2023.1-2024.12）

（5）重点实验室自主培育重点项目 在研 主持  （2023.9-2028.8）

  (6)  国家重点研发计划-政府间国家创新合作重点专项  项目骨干 （2024.6-2027.5）

（7）西藏自治区科学技术厅重点研发专项 项目骨干 （2025.1-2026.12）

主讲课程  本科生课程

•   《生物信息学原理》

•   《生物信息软件综合实践》

• 《写作与沟通：人工智能与生命科学》

主要研究论文：ORCiD http://orcid.org/0000-0001-8355-2959

一作(含共同一作^#) 或通讯作者（含共同通讯作者^*）文章

• 2026年

19. Lei Tan, Shenchao Zhu, Junli Ye, Wen-Biao Jiao. A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily. Mol. Biol. Evol. 2026, DOI: 10.1093/molbev/msag075   Accepted.

18. Jing Huang, Pei-Xuan Xiao, Ling Cui, Lei Tan, Shenchao Zhu, Junli Ye, Wen-Biao Jiao; Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of three Citrus genomes, Horticulture Research, 2026;, uhag048  

17. Pei-Xuan Xiao; Lei Tan; Jianke Dong; Jing Huang; Yuhong Huang; Jia-Bao He; Handong Su; Botao Song; Wen-Biao Jiao; Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome, Genome Biology, 2026, 27:70

• 2025年

16. Hu, J.*, Du, Z., Liu, C., Wen, H., Liu, C., Chen, P., Shi, C., Ye, J., Ji, Q. H., Deng, X., Bosch, M., Ling Z., Jiao WB.*, Chai L.* (2025). Pan-S-locus analysis reveals insights into the origin and evolution of self-incompatibility in the orange subfamily. Genome Biol. 26:344.

15. Lian Q*, Jiao W-B*, Wang Y*: Designing Better Crops with Phased Pangenomes. Mol. Plant 2025, doi:10.1016/j.molp.2025.08.014. 

14. Du Z-Z, He J-B, Xiao P-X, Hu J, Yang N, Jiao W-B: Varigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes. Mol. Plant2025, 18:1587–1601.

13.Du Z-Z, He J-B, Jiao W-B: Plant graph-based pangenomics: techniques, applications, and challenges. aBIOTECH 2025, doi:10.1007/s42994-025-00206-7.

12. Wang C, Tan L, Zhang Z, Li X, Xia L, Cao P, Tong H, Ou X, Li S, Zhang J,Li et al.: Haplotype-resolved genome reveals haplotypic variation and the biosynthesis of medicinal ingredients in Areca catechu L. Mol. Hortic 2025, 5:24.

11. Zuo H, Liu S, Tan L, Huang Y, Li Y, Gesang P, Hong Y, Deng X, Wang X, Xu Q, et al.: Chromosome-level assembly of Prunus serrula Franch genome. Sci Data 2025, 12:494.

• 2024年
  

10. Du, Z.-Z., He, J.-B., and Jiao, W.-B*. (2024). SynDiv: An efficient tool for chromosome collinearity-based population genomics analyses. Plant Commun. 2024, 5:101071. doi:https://doi.org/10.1016/j.xplc.2024.101071.

9.Du Z-Z, He J-B, Jiao W-B^*: A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25:91 https://doi.org/10.1186/s13059‑024‑03239‑1 

8. Song L, Huang Y, Zuo H, Tang N, Li Z, Jiao WB^*, Xu F^*, Xu Q^*, Chen Z^*: Chromosome-level assembly of triploid genome of sichuan pepper (Zanthoxylum armatum). Hortic Plant J 2024, 10:437–449.

• 2023年

7. Xiao P-X, Li Y, Lu J, Zuo H, Pingcuo G, Ying H, Zhao F, Xu Q, Zeng X, Jiao W-B^*: High-quality assembly and methylome of a Tibetan wild tree peony genome ( Paeonia ludlowii) reveal the evolution of giant genome architecture. Hortic Res 2023, 10.

• 2022年及以前

6. Sun H#, Jiao WB#, Krause K, Campoy JA, Goel M, Folz-Donahue K, Kukat C, Huettel B, Schneeberger K: Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nature Genetics 2022, 3:342-348

5. Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, et al. :The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Molecular Biology and Evolution 2021, 38:1225-1240

4. Jiao WB, Schneeberger K: Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nature Communications 2020, 11:989.

3. Jiao WB, Schneeberger K: The impact of third generation genomic technologies on plant genome assembly. Current Opinion Plant Biology 2017, 36:64-70.

2. Jiao WB, Garcia Accinelli G, Hartwig B, Kiefer C, Baker D, Severing E, Willing E-M, Piednoel M, Woetzel S, Madrid-Herrero E, et al.: Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research 2017, 27:778–786.

1. Jiao WB, Huang D, Xing F, Hu Y, Deng XX, Xu Q, Chen LL: Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant Journal 2013, 75:954–964.

合作参与文章

19. Fan Y-J, Du Z-Z, He X-Y, Liu Z-A, Zhuang J-X, Xiao G-A, Duan Y-Y, Tan F-Q, Xie K-D, Jiao W-B, et al.: Somatic variations in the meiosis-specific gene CrMER3 confer seedlessness in a citrus bud sport. J Integr Plant Biol 2025, n/a.

18. Liu S, Xu Y, Yang K, Huang Y, Lu Z, Chen S, Gao X, Xiao G, Chen P, Zeng X, et al.: Origin and de novo domestication of sweet orange. Nat Genet 2025, 57:754–762.

17. Hu S, Zeng X, Liu Y, Li Y, Qu M, Jiao W-B, Han Y, Kang C: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries. Genome Res 2024, 34:1582–1594.

16. Sun H, Abeli P, Campoy JA, Rütjes T, Krause K, Jiao W-B, Beaudry R, Schneeberger K: The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation. BMC Plant Biol 2024, 24:912.

15. Del Toro-De León, G., van Boven, J., Santos-González, J., Jiao, W.-B., Peng, H., Schneeberger, K., and Köhler, C. (2024). Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Res. Advance Access published July 5, 2024, doi:10.1093/nar/gkae572.

14. Hu J, Guo F, Du Z, Chen P, Shi C, Zhang J, Ye J, Deng X, Larkin RM, Jiao W, et al.: A rare inter-haplotypic recombination at the S-locus contributed to the loss of self-incompatibility in trifoliate orange. Plant Commun 2024, doi:10.1016/j.xplc.2024.100940.

13. Yuan-yuan LIU, Jian-ke D, Jing-wen Y, Wen-xiang MEI, Gang C, Jing-jing GUO: 利用野生种 Solanum boliviense 创制马铃薯抗寒种质. 作物学报 2024, doi:10.3724/SP.J.1006.2024.34159.

12. 宋波涛, 涂卫, 王海波, 董建科, 袁平平, 景晟林, 刘园园, 焦文标: 马铃薯种质演化与分类研究进展. 中国马铃薯 2023, 3:536–554.

11. Huang Y, He J, Xu Y, Zheng W, Wang S, Chen P, Zeng B, Yang S, Jiang X, Liu Z, et al.: Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat Genet 2023, 55:1964–1975.

10. Madrid E, Severing E, de Ansorena E, Kiefer C, Brand L, Martinez-Gallegos R, Woetzel S, Kemi U, Jiao WB, Schneeberger K, et al.: Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering. Proc. Natl. Acad. Sci.  2021, 118.

9. Campoy, J.A., Sun, H., Goel, M. Jiao WB, et al. Gamete binning: chromosome-level and haplotype- resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 21, 306 (2020). 

8. Goel M, Sun H, Jiao WB, Schneeberger K: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019, 20:277.

7. Dittberner H, Becker C, Jiao WB, Schneeberger K, Hölzel N, Tellier A, Meaux J: Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD‐seq analysis in floodplain Arabis species. Mol. Ecol. 2019, 28:3887–3901.

6. Kiefer C, Willing E-M, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K: Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. Nature Plants 2019, 5:846–855.

5. Zapata L, Ding J, Willing E, Hartwig B, Bezdan D, Jiao WB, Patel V, et al.: Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc. Natl. Acad. Sci. 2016, 113:E4052–E4060.

4. Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, et al.: Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci. Data 2016, 3:160076.

3. Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, et al.:  Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc. Natl. Acad. Sci. 2016, 113:E5163–E5171.

2. Gutjahr C, Gobbato E, Choi J, Riemann M, Johnston MG, Summers W, Carbonnel S, Mansfield C, Yang SY, Nadal M, Acosta I, Takano M, Jiao WB, et al.: Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science 2015, 350:1521–1524.

1. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, et al.: The draft genome of sweet orange (Citrus sinensis). Nature Genetics 2013, 45:59–66.