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Peer-reviewedCC BY 4.0Frontiers in Plant Science

The haplotype-resolved genome of Swinglea glutinosa and pangenome analysis provide insight into resistance to citrus Huanglongbing

  • Jiawen Wen1,2
  • Jin Xu1
  • Connor G. Hendrich1
  • Zhiqian Pang1
  • Nian Wang1,3
  1. 1Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida
  2. 2Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida
  3. 3Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida
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Abstract

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus ( C Las), is the most devastating citrus disease worldwide, and all commercial varieties are susceptible to HLB. Swinglea glutinosa , a citrus relative, is resistant to C Las, but the genetic basis of its HLB resistance remains unknown. We completed a high-quality, haplotype-phased chromosome-level genome of S. glutinosa. We conducted a pangenome analysis with 25 citrus and citrus-relative accessions and identified a pan-NLRome of nucleotide-binding domain leucine-rich repeat (NLR) immune receptors representing 19,476 NLR genes. Genes specific to HLB-resistant citrus genotypes were enriched for CoA-ligase activity and auxin transport, and HLB-resistant genotypes consistently carried fewer NLRs. S. glutinosa additionally showed significant expansion of Pathogenesis-Related Protein 1 ( PR1 ) genes, lineage-specific antimicrobial peptides, and unique genes enriched for the cullin-RING ubiquitin ligase complex. In susceptible Citrus sinensis most differential NLR expression occurred at late infection stages, predominantly among coiled-coil NLRs. A single core CNL orthogroup, expanded in C. sinensis and uniformly induced upon infection, accounted for most of this response, indicating that NLR expansion and induction are not sufficient for resistance to HLB. These results will support future functional studies of HLB resistance mechanisms and provide genomic information to facilitate development of HLB-resistant citrus varieties through traditional and biotechnological approaches.

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Cite

BibTeXRIS
BibTeX
@article{wen2026haplotyperesolved,
  title = {{The haplotype-resolved genome of Swinglea glutinosa and pangenome analysis provide insight into resistance to citrus Huanglongbing}},
  author = {Jiawen Wen and Jin Xu and Connor G. Hendrich and Zhiqian Pang and Nian Wang},
  journal = {Frontiers in Plant Science},
  year = {2026},
  month = oct,
  doi = {10.3389/fpls.2026.1988077},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1988077/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - The haplotype-resolved genome of Swinglea glutinosa and pangenome analysis provide insight into resistance to citrus Huanglongbing
AU  - Jiawen Wen
AU  - Jin Xu
AU  - Connor G. Hendrich
AU  - Zhiqian Pang
AU  - Nian Wang
PY  - 2026
DA  - 2026/10/14
JO  - Frontiers in Plant Science
DO  - 10.3389/fpls.2026.1988077
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2026.1988077/full
AB  - Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus ( C Las), is the most devastating citrus disease worldwide, and all commercial varieties are susceptible to HLB. Swinglea glutinosa , a citrus relative, is resistant to C Las, but the genetic basis of its HLB resistance remains unknown. We completed a high-quality, haplotype-phased chromosome-level genome of S. glutinosa. We conducted a pangenome analysis with 25 citrus and citrus-relative accessions and identified a pan-NLRome of nucleotide-binding domain leucine-rich repeat (NLR) immune receptors representing 19,476 NLR genes. Genes specific to HLB-resistant citrus genotypes were enriched for CoA-ligase activity and auxin transport, and HLB-resistant genotypes consistently carried fewer NLRs. S. glutinosa additionally showed significant expansion of Pathogenesis-Related Protein 1 ( PR1 ) genes, lineage-specific antimicrobial peptides, and unique genes enriched for the cullin-RING ubiquitin ligase complex. In susceptible Citrus sinensis most differential NLR expression occurred at late infection stages, predominantly among coiled-coil NLRs. A single core CNL orthogroup, expanded in C. sinensis and uniformly induced upon infection, accounted for most of this response, indicating that NLR expansion and induction are not sufficient for resistance to HLB. These results will support future functional studies of HLB resistance mechanisms and provide genomic information to facilitate development of HLB-resistant citrus varieties through traditional and biotechnological approaches.
SN  - 1664-462X
ER  -