Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. In plants, NLR proteins are important intracellular receptors with roles in innate immunity and disease resistance. This work provides a panoramic view of this diverse and complicated gene family in the model species A. thaliana and provides a foundation for the identification and functional study of disease-resistance genes in agronomically important species with complex genomes.
| Original language | English |
|---|---|
| Pages (from-to) | 1260-1272.e14 |
| Journal | Cell |
| Volume | 178 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 22 Aug 2019 |
Keywords
- disease resistance genes
- genomics
- innate immunity
- integrated domains
- NLR
- plant immunity
- RenSeq
- sequence capture
- SMRT sequencing
- targeted enrichment
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
Cite this
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. / Van de Weyer, Anna Lena; Monteiro, Freddy; Furzer, Oliver J.; Nishimura, Marc T.; Cevik, Volkan; Witek, K.; Jones, Jonathan D.G.; Dangl, Jeffery L.; Weigel, Detlef; Bemm, F.
In: Cell, Vol. 178, No. 5, 22.08.2019, p. 1260-1272.e14.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
AU - Van de Weyer, Anna Lena
AU - Monteiro, Freddy
AU - Furzer, Oliver J.
AU - Nishimura, Marc T.
AU - Cevik, Volkan
AU - Witek, K.
AU - Jones, Jonathan D.G.
AU - Dangl, Jeffery L.
AU - Weigel, Detlef
AU - Bemm, F.
PY - 2019/8/22
Y1 - 2019/8/22
N2 - Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. In plants, NLR proteins are important intracellular receptors with roles in innate immunity and disease resistance. This work provides a panoramic view of this diverse and complicated gene family in the model species A. thaliana and provides a foundation for the identification and functional study of disease-resistance genes in agronomically important species with complex genomes.
AB - Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. In plants, NLR proteins are important intracellular receptors with roles in innate immunity and disease resistance. This work provides a panoramic view of this diverse and complicated gene family in the model species A. thaliana and provides a foundation for the identification and functional study of disease-resistance genes in agronomically important species with complex genomes.
KW - disease resistance genes
KW - genomics
KW - innate immunity
KW - integrated domains
KW - NLR
KW - plant immunity
KW - RenSeq
KW - sequence capture
KW - SMRT sequencing
KW - targeted enrichment
UR - http://www.scopus.com/inward/record.url?scp=85070544705&partnerID=8YFLogxK
U2 - 10.1016/j.cell.2019.07.038
DO - 10.1016/j.cell.2019.07.038
M3 - Article
C2 - 31442410
AN - SCOPUS:85070544705
VL - 178
SP - 1260-1272.e14
JO - Cell
JF - Cell
SN - 0092-8674
IS - 5
ER -