Publications

Jhu MY*, Heffer J, Deamer A, Moraes TA, Piskorz AM, Xia C. Plant-Compatible Xenium In Situ Sequencing: Optimised Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules. bioRxiv. 2025:2025-07.

doi: https://doi.org/10.1101/2025.07.22.663073

Understanding how gene expression is regulated in space and time during plant organogenesis is crucial for crop improvement. However, spatial transcriptomics methods developed for animal systems often fail in plants due to rigid cell walls, autofluorescence, and vacuoles, which make sectioning and detection significantly more challenging. We present an optimised protocol for applying Xenium in situ sequencing to Medicago truncatula roots and nodules. The workflow includes tailored tissue preparation, sectioning, hybridisation, staining, imaging, and image analysis designed for plant samples. To improve sensitivity, we incorporated strategic codeword selection and developed a modular probe design: a 380-gene panel with a flexible 100-gene add-on, including orthologs from two Medicago ecotypes. Validation across multiple nodule stages with both a 50-gene panel and a 480-gene panel confirmed robust detection of diverse cell types and developmental markers. This protocol enables reproducible, high-resolution spatial transcriptomics in plants and provides a foundation for extending Xenium to other species and organs. 

Jhu MY, Oldroyd GED*. Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security? Plos Biology. 2023 Mar 14;21(3):e3001982. PMID: 36917569; PMCID: PMC10013914.

doi: https://doi.org/10.1371/journal.pbio.3001982

Jhu MY, Farhi M, Wang L, Philbrook RN, Belcher MS, Nakayama H, Zumstein KS, Rowland SD, Ron M, Shih PM, Sinha NR*. Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism. Plant Physiology. 2022 May 3;189(1):129-151. PMID: 35099559; PMCID: PMC9070836.

doi: https://doi.org/10.1093/plphys/kiac024

Parasitic plants of the genus Cuscuta (dodders) cause severe crop losses worldwide by forming haustoria that invade host tissues and siphon resources. While most cultivated tomatoes are highly susceptible, certain Heinz hybrid cultivars display resistance in the field. The underlying mechanism, however, was unknown. In this study, we discovered that resistant Heinz lines deploy a lignin-based defence response localised to the stem cortex at the site of Cuscuta campestris attachment. This targeted lignification prevents parasite penetration into host vascular tissues. Through genetic and transcriptomic analyses, we identified key regulators of this resistance: Lignin Induction Factor 1 (LIF1), SlMYB55, and the CC-NBS-LRR gene CuRLR1, which mediate lignification, while SlWRKY16 acts as a potential negative regulator of LIF1. CuRLR1 may also function in the perception of Cuscuta-derived signals. These findings reveal a molecular framework for lignin-based host resistance and provide a foundation for developing parasite-resistant crops through breeding or biotechnology.

Jhu MY, Ichihashi Y, Farhi M, Wong C, Sinha NR*. LATERAL ORGAN BOUNDARIES DOMAIN 25 functions as a key regulator of haustorium development in dodders. Plant Physiology. 2021 Aug 3;186(4):2093-2110. PMID: 34618110; PMCID: PMC8331169.

doi: https://doi.org/10.1093/plphys/kiab231

The stem parasitic plant Cuscuta campestris (dodder) invades host tissues and extracts nutrients through haustoria. To investigate the genetic regulation, we profiled transcriptomes from six Cuscuta tissues and identified LATERAL ORGAN BOUNDARIES DOMAIN 25 (CcLBD25) as highly expressed in prehaustoria and haustoria. Gene co-expression networks and laser-capture microdissection RNA-seq indicated CcLBD25 regulates cell wall loosening, organ initiation, and auxin-mediated signalling. Functional studies using host-induced gene silencing in tomato showed that down-regulation of CcLBD25 impaired prehaustorium formation, reduced pectin digestion, prevented searching hyphae development, and blocked vascular connections with the host. Parasites growing on CcLBD25 RNAi hosts exhibited reduced biomass and premature flowering, consistent with nutrient stress. These results establish CcLBD25 as a key transcriptional regulator of haustorium organogenesis. The discovery also supports the hypothesis that stem parasitic plants co-opted both shoot- and root-derived developmental programs for haustorium formation, offering insights into parasitic plant evolution and strategies for engineering crop resistance. 

Jhu MY*, Sinha NR*. Cuscuta species: Model organisms for haustorium development in stem holoparasitic plants. Frontiers in Plant Science. 2022 Dec 12;13:1086384. PMID: 36578337; PMCID: PMC9792094.

doi: https://doi.org/10.3389/fpls.2022.1086384