Rachelle Lee Rui Qi

@nus.edu.sg

Research Fellow, Department of Biological Sciences
National University of Singapore

Rachelle Lee Rui Qi


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https://researchid.co/rachellelee

EDUCATION

National University of Singapore, PhD

RESEARCH INTERESTS

genetics, bioinformatics
9

Scopus Publications

120

Scholar Citations

3

Scholar h-index

2

Scholar i10-index

Scopus Publications

  • Decoding Arabidopsis growth-defense trade-offs through ADR1-associated transcriptional networks
    Donghui Hu, Jinge Wang, Rachelle R.Q. Lee, Zezhao Su, Wangsheng Zhu, et al.
    Cell Reports, 2026
  • Some assembly required: Modularity and programmability as keys to decoupling growth-defence trade-offs in plants
    Rachelle R.Q. Lee, Donghui Hu, Eunyoung Chae
    Current Opinion in Plant Biology, 2026
  • Plant science for sustainability: by and for future generations
    Rini Rahiman, Karthikbabu Kannivadi Ramakanth, Rachelle Rui Qi Lee, Felicia Wei Shan Leong, Hong Jhun Sim, et al.
    New Phytologist, 2025
  • Structural determinants of DANGEROUS MIX 3, an alpha/beta hydrolase that triggers NLR-mediated genetic incompatibility in plants
    Wei-Lin Wan, Gijeong Kim, Nayun Kim, Yi Yun Tan, Machiko Watari, et al.
    Molecular Cell, 2025
  • Monkeys at Rigged Typewriters: A Population and Network View of Plant Immune System Incompatibility
    Rachelle R.Q. Lee, Eunyoung Chae
    Annual Review of Plant Biology, 2025
    Immune system incompatibilities between naturally occurring genomic variants underlie many hybrid defects in plants and present a barrier for crop improvement. In this review, we approach immune system incompatibilities from pan-genomic and network perspectives. Pan-genomes offer insights into how natural variation shapes the evolutionary landscape of immune system incompatibilities, and through it, selection, polymorphisms, and recombination resistance emerge as common features that synergistically drive these incompatibilities. By contextualizing incompatibilities within the immune network, immune receptor promiscuity, complex dysregulation, and single-point failure appear to be recurrent themes of immune system defects. As geneticists break genes to investigate their function, so can we investigate broken immune systems to enrich our understanding of plant immune systems and work toward improving them.
  • Generation of Inheritable A-to-G Transitions Using Adenine Base Editing and NG-PAM Cas9 in Arabidopsis thaliana
    Yi Yun Tan, Yin Yin Liew, Rachelle R. Q. Lee, Baptiste Castel, Nga Man Chan, et al.
    Molecular Plant Microbe Interactions, 2025
    Towards precise genome editing, base editors have been developed by fusing catalytically compromised Cas9 with deaminase components, mediating C-to-T (cytosine base editors) or A-to-G (adenine base editors) transition. We developed a set of vectors consisting of a 5′-NG-3′ PAM-recognizing variant of SpCas9 with adenosine deaminases TadA7.10 or TadA8e. Using a phenotype-based screen in Arabidopsis thaliana targeting multiple PDS3 intron splice sites, we achieved up to 81% somatic A-to-G editing in primary transformants at a splice acceptor site with NGG PAM, while 35% was achieved for the same target adenine with NGA PAM. Among tested vectors, pECNUS4 (Addgene #184887), carrying TadA8e, showed the highest adenine base editor (ABE) efficiency. With pECNUS4, we recreated a naturally occurring allele of DANGEROUS MIX3 ( DM3) in two generations, transgene-free, for NGC PAM. We also simultaneously base-edited four redundant DM1/SSI4 homologs, encoding nucleotide-binding leucine-rich repeat (NLR) proteins, using a single gRNA with NGA PAM targeting the conserved yet functionally crucial P-loop motif of NLR proteins. We found fixation of A-to-G in three NLR genes for all three possible adenine sites within base-editing window 3-9, as the edited genes segregate in T2. Multigene targeting succeeded in rescuing the previously reported autoimmune phenotype in two generations. Mediating desired ABE on seven NLR genes simultaneously was successful as well; above 77% editing was achieved in six of the seven possible targets in a T1 plant, with the remaining having a moderately high (32%) editing. ABE application to specifically inactivate functional motifs is anticipated to expedite the discovery of novel roles for proteins. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
  • Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg
    Rachelle R Q Lee, Wei Yuan Cher, Jinge Wang, Yujie Chen, Eunyoung Chae
    Nucleic Acids Research, 2023
    MINORg is an offline gRNA design tool that generates the smallest possible combination of gRNA capable of covering all desired targets in multiple non-reference genomes. As interest in pangenomic research grows, so does the workload required for large screens in multiple individuals. MINORg aims to lessen this workload by capitalising on sequence homology to favour multi-target gRNA while simultaneously screening multiple genetic backgrounds in order to generate reusable gRNA panels. We demonstrated the practical application of MINORg by knocking out 11 homologous genes tandemly arrayed in a multi-gene cluster in two Arabidopsis thaliana lineages using three gRNA output by MINORg. We also described a new PCR-free modular cloning system for multiplexing gRNA, and used it to knockout three tandemly arrayed genes in another multi-gene cluster with gRNA designed by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.
  • A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana
    Ana Cristina Barragan, Maximilian Collenberg, Jinge Wang, Rachelle R Q Lee, Wei Yuan Cher, et al.
    Molecular Biology and Evolution, 2021
    Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR–PL (leucine-rich repeat [LRR]–post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain—a region from which the DM10 risk haplotype is absent—indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
  • Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes
    Rachelle R.Q. Lee, Eunyoung Chae
    Plant Communications, 2020

RECENT SCHOLAR PUBLICATIONS

  • Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg
    RRQ Lee, WY Cher, J Wang, Y Chen, E Chae
    Nucleic Acids Research 51 (8), e43-e43 , 2023
    2023
    Citations: 6
  • A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana
    AC Barragan, M Collenberg, J Wang, RRQ Lee, WY Cher, FA Rabanal, ...
    Molecular Biology and Evolution 38 (2), 557-574 , 2021
    2021
    Citations: 47
  • Variation patterns of NLR clusters in Arabidopsis thaliana genomes
    RRQ Lee, E Chae
    Plant communications 1 (4), 100089 , 2020
    2020
    Citations: 66
  • A singleton NLR of recent origin causes hybrid necrosis in Arabidopsis thaliana
    AC Barragan, M Collenberg, J Wang, RRQ Lee, WY Cher, FA Rabanal, ...
    BioRxiv , 2020
    2020
    Citations: 1
  • Structural and Biochemical Study of DANGEROUS MIX pairs in Arabidopsis thaliana
    N Charoennit, G Kim, WL Wan, YY Liew, J Wang, R Lee, Y Zhang, ...
    2019 IS-MPMI XVIII Congress , 2019
    2019
  • Characterization of autoimmunity triggered by DANGEROUS MIX pairs in Arabidopsis thaliana
    WL Wan, YY Liew, N Charoennit, J Wang, R Lee, Y Zhang, E Chae
    2019 IS-MPMI XVIII Congress , 2019
    2019

MOST CITED SCHOLAR PUBLICATIONS

  • Variation patterns of NLR clusters in Arabidopsis thaliana genomes
    RRQ Lee, E Chae
    Plant communications 1 (4), 100089 , 2020
    2020
    Citations: 66
  • A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana
    AC Barragan, M Collenberg, J Wang, RRQ Lee, WY Cher, FA Rabanal, ...
    Molecular Biology and Evolution 38 (2), 557-574 , 2021
    2021
    Citations: 47
  • Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg
    RRQ Lee, WY Cher, J Wang, Y Chen, E Chae
    Nucleic Acids Research 51 (8), e43-e43 , 2023
    2023
    Citations: 6
  • A singleton NLR of recent origin causes hybrid necrosis in Arabidopsis thaliana
    AC Barragan, M Collenberg, J Wang, RRQ Lee, WY Cher, FA Rabanal, ...
    BioRxiv , 2020
    2020
    Citations: 1
  • Structural and Biochemical Study of DANGEROUS MIX pairs in Arabidopsis thaliana
    N Charoennit, G Kim, WL Wan, YY Liew, J Wang, R Lee, Y Zhang, ...
    2019 IS-MPMI XVIII Congress , 2019
    2019
  • Characterization of autoimmunity triggered by DANGEROUS MIX pairs in Arabidopsis thaliana
    WL Wan, YY Liew, N Charoennit, J Wang, R Lee, Y Zhang, E Chae
    2019 IS-MPMI XVIII Congress , 2019
    2019