Portrait photo of Jian-Feng Mao taken in a greenhouse with trees in the backgroundPhoto: Mattias Pettersson Surfing the data ocean of plant genomes, we (data analysts) are discovering hidden intricacies (genome sequencing and assembly), investigating what it looks like (annotation and characterization), where and why they are there (evolutionary inference), and predicting what, when and how it will be (functional exploitation, genomic predication).

Our research interests lie in plant genomics and tree breeding, particularly in genome evolution and genomic mechanisms of various biological processes such as secondary metabolite biosynthesis and biotic/abiotic response, allele-specific gene expression. We are also keen on implementing computation-intensive multi-omics tools/strategies in dissecting complex systems to support efficient investigation, manipulation and breeding. We finished several high-quality genome assemblies for a wide-range of plant species, including a de novo genome assembly with contig N50>50 Mb for a conifer species (Cupressaceae) with ~10 Gb genome size, T2T gap-less genome assembly for two poplar species by sequencing an interspecific F1 hybrid, chromosome-scale genome assembly for yellowhorn, ginger, azaleas, oak, lilac and tetraploid Salvia splendens.

We developed a novel k-mer based genome software ( to assist chromosome assignment in allopolyploid and hybrids, and computational tools/pipelines for centromere identification (, lncRNA predication ( and allele-specific gene expression ( analyses.

Complex scientific illustration consisting of five individual graphs illustrating the experimental design, a time-ordered gene co-expression network for UV-B and UV-C, UV-B and UV-C, a short summary of the UV-B and UV-C response in pine and a illustration of the network comparison method

UV-B and UV-C responses in pine

Key publications

  • Nie, S., S.-W. Zhao, T.-L. Shi, W. Zhao, R.-G. Zhang, X.-C. Tian, J.-F. Guo, X.-M. Yan, Y.-T. Bao, Z.-C. Li, L. Kong, H.-Y. Ma, Z.-Y. Chen, H. Liu, Y. A. El-Kassaby, I. Porth, F.-S. Yang and J.-F. Mao (2023). "Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color." Horticulture Research 10(1): uhac241.
  • Jia, K. H., Z. X. Wang, L. Wang, G. Y. Li, W. Zhang, X. L. Wang, F. J. Xu, S. Q. Jiao, S. S. Zhou, H. Liu, Y. Ma, G. Bi, W. Zhao, Y. A. El-Kassaby, I. Porth, G. Li, R. G. Zhang and J. F. Mao (2022). "SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers." New Phytol 235(2): 801-809.
  • Xu, J., H. Luo, S. S. Zhou, S. Q. Jiao, K. H. Jia, S. Nie, H. Liu, W. Zhao, X. R. Wang, Y. A. El-Kassaby, I. Porth and J. F. Mao (2022). "UV-B and UV-C radiation trigger both common and distinctive signal perceptions and transmissions in Pinus tabuliformis Carr." Tree Physiol 42(8): 1587-1600.
  • Jia, K. H., W. Zhao, P. A. Maier, X. G. Hu, Y. Jin, S. S. Zhou, S. Q. Jiao, Y. A. El-Kassaby, T. Wang, X. R. Wang and J. F. Mao (2020). "Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)." Evol Appl 13(4): 665-676.
  • Yang, F. S., S. Nie, H. Liu, T. L. Shi, X. C. Tian, S. S. Zhou, Y. T. Bao, K. H. Jia, J. F. Guo, W. Zhao, N. An, R. G. Zhang, Q. Z. Yun, X. Z. Wang, C. Mannapperuma, I. Porth, Y. A. El-Kassaby, N. R. Street, X. R. Wang, Y. Van de Peer and J. F. Mao (2020). "Chromosome-level genome assembly of a parent species of widely cultivated azaleas." Nat Commun 11(1): 5269.