Publications · Plant IDEA Lab

Publications are grouped by year. Entries and links are maintained directly in content/publication.md.

For Xianqing, Xuan, and Yi: # co-first author, * coresponding author

2026

Meng, Y., Chen, F., Lu, Y., Wang, L., Yi, K., Jia, X.*, & Yuan, Y.* (2026). Alternative splicing as an evolvable regulatory layer in plant adaptation and evolution. Horticulture Research, uhag453.
Lu, Y., Li, J., Yi, K., & Jia, X.* (2026). Programmable plant nutrition through synthetic transportome engineering. Journal of Plant Physiology, 326, 154874.
Song, J.-B., Li, Y.-R., Zhao, Z.-X., Zuo, X.-Z., Wang, C.-F., Huang, M., Liu, S.-F., Chen, Y.-F., Song, W.-Q., Wang, L., Wang, Y.-J., & Huang, X.* (2026). Integrated transcriptomic and metabolomic analyses reveal the involvement of AtGASA1 and AtGASA4 in salicylic acid pathway-associated immune responses in Arabidopsis. Plant Science, 371, 113246.
Li, T., Wang, X., Yao, X., Liu, Y., Song, M., Mi, Y., Yang, H., Liu, L., Li, E., Sun, J., Yu, H., Ohad, N., Huang, X.*, Liu, F., & Xue, Y. (2026). Capsicum annuum TC48 shows both resistance and tolerance to cucumber mosaic virus and is a potential genetic resource for pepper improvement. aBIOTECH, 100081.
Song, J.-B., He, H.-E., Wang, C.-F., Zuo, X.-Z., Zhao, Z.-X., Li, Y.-R., Chen, Y.-F., Liu, S.-F., Guo, H.-W., & Huang, X.* (2026). AtGASA1 positively regulates Arabidopsis response to salt stress by suppressing accumulation of reactive oxygen species. Plant Cell Reports, 45(5), 126.
Gao, H., Pan, L., Chen, A., Xing, X., Chen, Q., Wang, Y., & Huang, X.* (2026). Extracellular Vesicles: Key Mediators of Bioactive Molecule Transport in Plant–Microbe Interactions. Molecular Plant Pathology, 27(7), e70314.
Hu, G., Wang, M., Yangjin, L., Du, M., He, T., Jia, X.*, & Duan, R. (2026). Multi-omics insights into the woolly trait of Saussurea medusa and the plant’s coordinated regulation of flavonoid biosynthesis. Communications Biology.
Yu, J., Zhao, Y., Hu, G., Fu, J., Xu, L., Yi, K., Jia, X.*, & Wang, L. (2026). Interplay between salicylic acid and plant nutrient homeostasis. Plant Hormones, 2(1).
Yuan, S., Yang, Y., Wang, X., Shao, S., Jia, X., Zhu, Y., Luo, B., & Yu, J. (2026). Surface-adsorbed phosphorus buffers environmental phosphate availability and influences phosphorus uptake in Chlamydomonas reinhardtii. Environmental Technology & Innovation, 104877.
Yuan, S., Yang, Y., Zhu, Y., Jia, X., & Yu, J. (2026). Multi-Omics Reveals Domestication-Associated Shifts in Phosphorus Adaptation Strategies in Tomato. Plants, 15(5), 820.
YangJin, L., Yuan, Y.#, Zeng, S., Hu, G., Du, M., Xiong, H., Jia, X.*, & Duan, R. (2026). Adaptive genome evolution and metabolic rewiring in the highland poppy Meconopsis integrifolia. Horticulture Research, 13(5), uhag045.

2025

Liu, Y., Mi, Y., Song, M., Yang, H., Liu, L., Yin, Q., Yao, X., Yu, G., Fu, Y., Qin, G., Liu, F., Huang, X.*, & Xue, Y. (2025). Features of DNA methylome in Capsicum spp. Epigenetics & Chromatin, 19(1), 2.
Zhang, S., Wang, Y., Lu, Y., Yuan, S., Wang, L., Xu, L., Yi, K., & Jia, X.* (2025). Plant STOP1 family: A helmsman in the soil multiple stress adaptation. Plant and Soil, 10.1007/s11104-025-07807-7.
Custódio, V., Salas-González, I., Gopaulchan, D., Flis, P., Amorós-Hernández, R., Gao, Y.-Q., Jia, X., Moreno, Â., Carrera, E., Marcon, C., Hochholdinger, F., Margarida Oliveira, M., Salt, D. E., & Castrillo, G. (2025). Individual leaf microbiota tunes a genetic regulatory network to promote leaf growth. Cell Host & Microbe, 33(3), 436-450.e15.

News & Commentary: Gourion, B. (2025). Plant growth promotion through repression of defenses by leaf microbiota. Cell Host & Microbe, 33(3), 325–326.
Yu, J., Luo, B., Yang, Y,, Ren, S., Xu, L., Wang, L., Jia, X., Zhu, Y., & Yi, K. (2025). Polyphosphate-enriched algae fertilizer as a slow-release phosphorus resource could improve plant growth and soil health. Journal of Integrative Agriculture, 24(9), 3656–3670.
Xu, Z., Jia, X.#, Li, R., Wang, L., Xu, L., & Yi, K. (2025). The basal level of salicylic acid represses the PRT6 N-degron pathway to modulate root growth and stress response in rice. Plant Communications, 6(4), 101239. [Data]
Jia, X.#*, Xu, Z., Xu, L., Frene, J. P., Gonin, M., Wang, L., Yu, J., Castrillo, G., & Yi, K. (2025). Identification of new salicylic acid signaling regulators for root development and microbiota composition in plants. Journal of Integrative Plant Biology, 67(2), 345–354. [Data]

2024

Zhao, B., Jia, X.#, Yu, N., Murray, J., Yi, K., & Wang, E. (2024) Microbe-dependent and independent nitrogen and phosphate acquisition in plants. New Phytologist, 242(4), 1507–1522. Featured article ESI highly cited

2023

Yu, J., Wang, L., Jia, X., Wang, Z., Yu, X., Ren, S., Yang, Y., Ye, X., Wu, X., Yi, K., & Zhu, Y. (2023). Different microbial assembly between cultivated and wild tomatoes under P stress. Soil Science and Environment, 2(1), SSE-2023-0010.
Jia, X., Wang, L., and Yi, K. (2023). Crosstalk between phosphate and other nutrients. In Plant Phosphorus Nutrition (CRC Press: Boca Raton). pp.48–58. (Book chapter)
Yang, Y., Ren, S., Jia, X., Zeng, H., Wang, L., Zhu, Y., & Yi, K. (2023). Measurement of total phosphorus and polyphosphate in Chlamydomonas reinhardtii. Bio-Protocol, 13(11), e4692.
Dai, S., Wu, H., Chen, H., Wang, Z., Yu, X., Wang, L., Jia, X., Qin, C., Zhu, Y., Yi, K., & Zeng, H. (2023). Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice. Plant Physiology and Biochemistry, 197, 107642.
Wang, L., Jia, X.#*, Xu, L., Yu, J., Ren, S., Yang, Y., Wang, K., López-Arredondo, D., Herrera-Estrella, L., Lambers, H., & Yi, K. (2023). Engineering microalgae for water phosphorus recovery to close the phosphorus cycle. Plant Biotechnology Journal, 21, 1373–1382. [Data]
Xu, L., Zhao, H., Wang, J., Wang, X., Jia, X., Wang, L., Xu, Z., Li, R., Jiang, K., Chen, Z., Luo, J., Xie, X., & Yi, K. (2023). AIM1-dependent high basal salicylic acid accumulation modulates stomatal aperture in rice. New Phytologist, 238(4), 1420–1430. [bioRxiv]
Jia, X., Wang, L., Nussaume, L., & Yi, K. (2023). Cracking the code of plant central phosphate signaling. Trends in Plant Science, 28(3), 267–270. [Data] Featured article
Jia, X., Wang, L., Zhao, H., Zhang, Y., Chen, Z., Xu, L., & Yi, K. (2023). The origin and evolution of salicylic acid signaling and biosynthesis in plants. Molecular Plant, 16(1), 245–259. [Data] Featured article ESI highly cited

News & Commentary: Wang, C., Gong, Z., & Han, G.-Z. (2023). On the origins and evolution of phytohormone signaling and biosynthesis in plants. Molecular Plant, 16(3), 511–513.

2022

Yuan, Y., Li, X., Yao, X., Fu, X., Cheng, J., Shan, H., Yin, X., & Kong, H. (2023). Mechanisms underlying the formation of complex color patterns on Nigella orientalis (Ranunculaceae) petals. New Phytologist, 237(6), 2450–2466.
Guo, M., Zhang, Y., Jia, X.#, Wang, X., Zhang, Y., Liu, J., Yang, Q., Ruan, W., & Yi, K. (2022). Alternative splicing of REGULATOR OF LEAF INCLINATION 1 modulates phosphate starvation signaling and growth in plants. The Plant Cell, 34, 3319–3338. [Data] Featured article ESI highly cited

News & Commentary: Frungillo, L. (2022). Alternative splicing in plants: An elegant strategy to deal with an inconstant Pi. The Plant Cell, 34, 3162–3163.
Zhang, Y., Wang, L., Guo, Z., Xu, L., Zhao, H., Zhao, P., Ma, C., Yi, K., & Jia, X.* (2022). Revealing the underlying molecular basis of phosphorus recycling in the green manure crop Astragalus sinicus. Journal of Cleaner Production, 341, 130924. [Data] [News]
Wang, X., Wang, B., Song, Z., Zhao, L., Ruan, W., Gao, Y., Jia, X.*, & Yi, K. (2022). A spatial-temporal understanding of gene regulatory networks and NtARF-mediated regulation of potassium accumulation in tobacco. Planta, 255(1), 9. [Data]

2021

Yu, L., Ma, S., Zhang, X., Tian, D., Yang, S., Jia, X.*, & Traw, M. B. (2021). Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication. The Plant Journal, 108(5), 1365–1381.
Huo, Y., Zhao, Y., Xu, L., Yi, H., Zhang, Y., Jia, X., Zhao, H., Zhao, J., & Wang, F. (2021). An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions. BMC Bioinformatics, 22(1), 429.
Jia, X., Wang, L., Zeng, H., & Yi, K. (2021). Insights of intra/intercellular phosphate transport and signaling in unicellular green algae and multicellular land plants. New Phytologist, 232(4), 1566–1571. Featured article
Wang, L., Jia, X.#, Zhang, Y., Xu, L., Menand, B., Zhao, H., Zeng, H., Dolan, L., Zhu, Y., & Yi, K. (2021). Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants. Molecular Plant, 14(5), 838–846. [Data]
Jia, X., Zhang, Q., Jiang, M., Huang, J., Yu, L., Traw, M. B., Tian, D., Hurst, L. D., & Yang, S. (2021). Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation. PLOS Biology, 19(3), e3001164.
Yao, J.-W., Ma, Z., Ma, Y.-Q., Zhu, Y., Lei, M.-Q., Hao, C.-Y., Chen, L.-Y., Xu, Z.-Q., & Huang, X.* (2021). Role of melatonin in UV-B signaling pathway and UV-B stress resistance in Arabidopsis thaliana. Plant, Cell & Environment, 44(1), 114–129.
Zhou, Q., Meng, Q., Tan, X., Ding, W., Ma, K., Xu, Z., Huang, X.*, & Gao, H. (2021). Protein Phosphorylation Changes During Systemic Acquired Resistance in Arabidopsis thaliana. Frontiers in Plant Science, 12.
Zhu, Y., Guo, M.-J., Song, J.-B., Zhang, S.-Y., Guo, R., Hou, D.-R., Hao, C.-Y., An, H.-L., & Huang, X.* (2021). Roles of Endogenous Melatonin in Resistance to Botrytis cinerea Infection in an Arabidopsis Model. Frontiers in Plant Science, 12.

2020 and before

Jia, X., Yu, L., Tang, M., Tian, D., Yang, S., Zhang, X., & Traw, M. B. (2020). Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice. Journal of Plant Physiology, 248, 153141.
Wang, L., Ji, Y., Hu, Y., Hu, H., Jia, X., Jiang, M., Zhang, X., Zhao, L., Zhang, Y., Jia, Y., Qin, C., Yu, L., Huang, J., Yang, S., Hurst, L. D., & Tian, D. (2019). The architecture of intra-organism mutation rate variation in plants. PLOS Biology, 17(4), e3000191.
Jia, X., Zhang, Y., Zhang, Q., Zhao, Q., Traw, M. B., Wang, L., Tian, D., Wang, C., & Yang, S. (2019). High-resolution insight into recombination events at the SD1 locus in rice. The Plant Journal, 97(4), 683–692.
Liu, J., Niu, Y., Zhang, J., Zhou, Y., Ma, Z., & Huang, X.* (2018). Ca2+ channels and Ca2+ signals involved in abiotic stress responses in plant cells: Recent advances. Plant Cell, Tissue and Organ Culture (PCTOC), 132(3), 413–424.
Memon, S., Jia, X.#, Gu, L., & Zhang, X. (2016). Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana. BMC Evolutionary Biology, 16(1), 25.
Huang, X., Yao, J., Zhao, Y., Xie, D., Jiang, X., & Xu, Z. (2016). Efficient Rutin and Quercetin Biosynthesis through Flavonoids-Related Gene Expression in Fagopyrum tataricum Gaertn. Hairy Root Cultures with UV-B Irradiation. Frontiers in Plant Science, 7.
Huang, X., Wang, J., Du, Z., Zhang, C., Li, L., & Xu, Z. (2013). Enhanced resistance to stripe rust disease in transgenic wheat expressing the rice chitinase gene RC24. Transgenic Research, 22(5), 939–947.