Open Access
Open Access Resources
The data hosted on this page are open access resources freely available to the scientific community to use and analyze for research purposes.
Resistance Gene Discovery Project
This research was funded by the Gordon and Betty Moore Foundation through Grant GBMF4725 from 2015-2019.
The Challenge
Plants contain a broad repertoire of immune receptors (R genes) that mediate recognition of disease-causing organisms (pathogens). The major class of Rgenes is the NB-LRR (nucleotide-binding, leucine rich repeat) type, and an individual plant contains hundreds of different receptors. Activation of an NB-LRR receptor by a pathogen generally results in resistance to that pathogen, so the complement of NB-LRRs a plant possesses is a major determinant of which diseases it resists or succumbs to. Both pathogens and R genes evolve rapidly. Knowledge of R gene diversity within and across species would provide insight into the evolution of these important genes, improve our understanding of plant resistance, and aid the development of disease-resistant crops. However, the diversity of NB-LRRs within a given species and across related species is still poorly understood. Despite the advances in genome sequencing and explosion of available sequence data, until recently NB-LRR genes have been hard to sequence and annotate for technical reasons, because they are relatively similar to one another and are often found in clusters of highly similar alleles.
The Strategy
Scientists at the Sainsbury Laboratory in Norwich developed a fast, accurate, and cost-efficient technique for isolating and sequencing just the NB-LRR genes from a plant. Using this method, termed Resistance Gene Enhancement Sequencing (RenSeq), our collaborators sequenced resistance genes from hundreds of different plants within three important plant families. The analysis focused on crop plants and their wild relatives in three important plant families: the Solanaceae (tomatoes, potatoes, and their relatives) Triticeae (wheat, barley and related grains) and Brassicaceae (mustard greens, cabbage, turnips, canola and their relatives). The analysis included different individual isolates from a given species that evolved in different places in order to elucidate the diversity within species as well as between species. The results are publicly available in a database (below) to assist others analyzing or breeding for disease resistance in these species.
The Science
Our collaborators used the large dataset to answer important questions about R gene evolution, such as whether certain R gene families are evolving rapidly under pathogen pressure, whether some R genes have costs to the host plant in the absence of pathogen pressure, whether some classes of R genes have been selected or lost during domestication of crops, and whether there are novel classes of R genes that have not yet been described.
PROJECT: AT A GLANCE
CROP
Solanaceae (tomatoes, potatoes, and their relatives) Triticeae (wheat, barley and related grains) and Brassicaceae (mustard greens, cabbage, turnips, canola and their relatives)
COLLABORATORS
Prof. Jeff Dangl, University of North Carolina
Prof. Jonathan Jones, Sainsbury Laboratory, UK
Prof. Brian Staskawicz, University of California, Berkeley
Prof. Dr. Detlef Weigel, Max Planck Institute for Developmental Biology, Germany
FUNDING SUPPORT
This project was funded by the Gordon and Betty Moore Foundation to 2Blades through Grant GBMF4725 from 2015-2019.
Arabidopsis thaliana
The collection of resistance genes from 69 accessions of Arabidopsis thaliana was sequenced as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratories of Detlef Weigel (MPI), Jeff Dangl (UNC), and Jonathan Jones (TSL) and conducted under the auspices of the 2Blades Foundation. The provided data contain circular consensus sequence (CCS) reads from Resistance Gene Enrichment Sequencing (Ren-Seq) produced on the PacBio platform. These reads were subsequently assembled into contigs.
Additional resources related to this data set are described and linked in Van der Weyer et al., 2019.
DOWNLOAD
(Data hosted at Max Planck Institute for Developmental Biology Tübingen)
Nicotiana and Solanum species
The collection of resistance genes from four species of Nicotiana and four Solanum species were sequenced as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Jonathan Jones (TSL) and conducted under the auspices of the 2Blades Foundation. The data were uploaded to European Nucleotide Archive (ENA) and contain subreads from Resistance Gene Enrichment Sequencing (RenSeq) produced on the PacBio platform.
| Species | Sample | NCBI Accession |
|---|---|---|
| Nicotiana tabacum | ERS1972100 (SAMEA104347122) | ERX2225148 |
| Nicotiana sylvestris | ERS1972101 (SAMEA104347123) | ERX2225149 |
| Nicotiana tomentosiformis | ERS1972102 (SAMEA104347124) | ERX2225150 |
| Solanum tuberosum Group Phureja | ERS1972103 (SAMEA104347125) | ERX2225151 |
| Solanum tuberosumcv Maris Piper | ERS1972104 (SAMEA104347126) | ERX2225152 |
| Solanum lycopersicum accession FLA8059 | ERS1972105 (SAMEA104347127) | ERX2225153 |
| Solanum americanum accession 944750095 | ERS1972106 (SAMEA104347128) | ERX2225154 |
| Nicotiana benthamiana | ERS1972107 (SAMEA104347129) | ERX2225147 |
Tomatoes and other Solanaceae
The collection of resistance genes from tomato, pepper, N. benthamiana and wild Solanum species were sequenced as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Brian Staskawicz and conducted under the auspices of the 2Blades Foundation. The data were uploaded to the National Center for Biotechnology Information (NCBI) under the BioProject PRJNA496490 and contain circular consensus sequence (CCS) reads from Resistance Gene Enrichment Sequencing (RenSeq) produced on the PacBio platform.
Restrictions on data use
You are welcome to use these data to advance your studies of the plant immune system.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a genome-wide, whole-assembly scale prior to publication by the producers (Reserved Analyses). Reserved Analyses include the identification of complete sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and comparisons with other Solanaceae.
The embargo on publication of Reserved Analyses by researchers outside of the pan-NLR’ome Project is expected to extend until a first publication of the results of the project is accepted. Academic users are free to publish papers dealing with specific genes or small sets of genes. If these data are used for publication, please contact the responsible persons below to determine the acknowledgement.
| Species | NCBI Accession |
|---|---|
| S. lycopersicum Heinz | SRX4891006 |
| S. cheesmaniae 0422 | SRX4891000 |
| S. cheesmaniae 1039 | SRX4891003 |
| S. chmielewskii 1316 | SRX4891008 |
| S. chmielewskii 1330 | SRX4891001 |
| S. galapagense 0483 | SRX4891007 |
| S. galapagense 1136 | SRX4891004 |
| S. neorickii 1716 | SRX4891009 |
| S. pimpinellifolium 0722 | SRX4891005 |
| S. pimpinellifolium 1269 | SRX4891002 |
| C. annuum ECW | SRX4891011 |
| C. annuum ECW 20R | SRX4891012 |
| N. benthamiana | SRX4891010 |
Rice
NLR-encoding genes were sequenced from 66 accessions of Oryza sativa as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Jonathan Jones (TSL) in collaboration with Jean-Benoit Morel and Thomas Kroj (INRA) and managed by the 2Blades Foundation. Data were obtained via Resistance Gene Enrichment Sequencing (Ren-Seq) for 14 accessions via PacBio circular consensus sequence (CCS) and for 61 accessions (including those 14) via paired end Illumina reads on the HighSeq 2500 platform.
Restrictions on data use
You are welcome to use these data to advance your studies of the plant immune system.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a genome-wide, whole-assembly scale prior to publication by the producers (Reserved Analyses). Reserved Analyses include the identification of complete sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and comparisons with other Poaceae.
The embargo on publication of Reserved Analyses by researchers outside of the pan-NLR’ome Project is expected to extend until a first publication of the results of the project is accepted. Academic users are free to publish papers dealing with specific genes or small sets of genes. If these data are used for publication, please contact the responsible persons below to determine the acknowledgement.
All rice sequences can be downloaded through ENA under projects PRJEB23459and PRJEB29200.
| Rice Variety | Sample Accession |
|---|---|
| K1_Xiaogu | SAMEA104389502 (ERS2007444) |
| K8_Xiaogu | SAMEA104389503 (ERS2007445) |
| YYT72_Zinuo | SAMEA104389523 (ERS2007465) |
| P04_Baijao | SAMEA104389512 (ERS2007454) |
| T09_Acuce | SAMEA104389518 (ERS2007460) |
| YYT73_Acuce | SAMEA104389524 (ERS2007466) |
| V18_Baijao | SAMEA104389521 (ERS2007463) |
| YYT31_Acuce | SAMEA104389522 (ERS2007464) |
| E1_Hongjiao | SAMEA104389492 (ERS2007434) |
| Q7_Acuce | SAMEA104389514 (ERS2007456) |
| G9_Hongjiao | SAMEA104389495 (ERS2007437) |
| G13_Hongjiao | SAMEA104389494 (ERS2007436) |
| H15_Hongjiao | SAMEA104389497 (ERS2007439) |
| R17_Acuce | SAMEA104389515 (ERS2007457) |
| J05_Hongyang2 | SAMEA104389501 (ERS2007443) |
| M10_Acuce | SAMEA104389506 (ERS2007448) |
| S10_Acuce | SAMEA104389516 (ERS2007458) |
| B05_Baijao | SAMEA104389489 (ERS2007431) |
| V11_Baijao | SAMEA104389520 (ERS2007462) |
| F22_Hongjiao | SAMEA104389493 (ERS2007435) |
| H05_Hongjiao | SAMEA104389496 (ERS2007438) |
| HYYT76B_Huangpinuo | SAMEA104389498 (ERS2007440) |
| YYT78_Huangpinuo | SAMEA104389526 (ERS2007468) |
| Maratelli | SAMEA104389507 (ERS2007449) |
| Padi_Boenor | SAMEA104389513 (ERS2007455) |
| Kasalath | SAMEA104389504 (ERS2007446) |
| Kitaake | SAMEA104389505 (ERS2007447) |
| IRAT13 | SAMEA104389500 (ERS2007442) |
| Tetep | SAMEA104389519 (ERS2007461) |
| Oryzica_Llanos_5 | SAMEA104389511 (ERS2007453) |
| Azucena | SAMEA104389488 (ERS2007430) |
| Moroberekan | SAMEA104389508 (ERS2007450) |
| IR64 | SAMEA104389499 (ERS2007441) |
| Sariceltik | SAMEA104389517 (ERS2007459) |
| Nipponbare | SAMEA104389509 (ERS2007451) |
| Chepugu | SAMEA4975981 (ERS2794052) |
| Lubaigu | SAMEA4975982 (ERS2794053) |
| Zaogu | SAMEA4975983 (ERS2794054) |
| Epugu | SAMEA4975984 (ERS2794055) |
| Jianshuigu | SAMEA4975985 (ERS2794056) |
| Honglueduolu | SAMEA4975986 (ERS2794057) |
| Mingliangyou 527 | SAMEA4975987 (ERS2794058) |
| Liangyou 2161 | SAMEA4975988 (ERS2794059) |
| Jinpinggu | SAMEA4975989 (ERS2794060) |
| Luhonggu | SAMEA4975990 (ERS2794061) |
| B06 Acuce | SAMEA4975991 (ERS2794062) |
| P03 Acuce | SAMEA4975992 (ERS2794063) |
| D15 Baijiao | SAMEA4975993 (ERS2794064) |
| D09 Baijiao | SAMEA4975994 (ERS2794065) |
| T18 Acuce | SAMEA4975995 (ERS2794066) |
| YYT31 Bijiaolaojing | SAMEA4975996 (ERS2794067) |
| F13 Hongjiao | SAMEA4975997 (ERS2794068) |
| E5 Hongjiao | SAMEA4975998 (ERS2794069) |
| J08 Hongyang 2 | SAMEA4975999 (ERS2794070) |
| J11 Hongyang 2 | SAMEA4976000 (ERS2794071) |
| L13 Xiaogu | SAMEA4976001 (ERS2794072) |
| M1 Xiaogu | SAMEA4976002 (ERS2794073) |
| YYT60 Xiaogu | SAMEA4976003 (ERS2794074) |
| YYT62 Xiaogu | SAMEA4976004 (ERS2794075) |
| YYT65 Xiaogu | SAMEA4976005 (ERS2794076) |
| YYT24 Xiaogu | SAMEA4976006 (ERS2794077) |
| YYT76B_Huangpinuo | SAMEA104389525 (ERS2007467) |
| NSF-TV116 | SAMEA104389510 (ERS2007452) |
| Cocodrie_301379 | SAMEA104389491 (ERS2007433) |
| C101A51 | SAMEA104389490 (ERS2007432) |
| Zhenshan2 | SAMEA104389527 (ERS2007469) |
Triticeae
Triticum aestivum (Bread wheat)
NLR-encoding genes were sequenced from 100 wheat landraces as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Jonathan Jones (TSL) in collaboration with Dr. Brande Wulff (John Innes Centre) and under the auspices of 2Blades Foundation. The data were uploaded to the European Nucleotide Archive and can be downloaded under project PRJEB35692
Restrictions on data use
You are welcome to use these data to advance your studies of the plant immune system.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a genome-wide, whole-assembly scale prior to publication by the producers (Reserved Analyses). Reserved Analyses include the identification of complete sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and comparisons with other Triticeae.
The embargo on publication of Reserved Analyses by researchers outside of the pan-NLR’ome Project is expected to extend until a first publication of the results of the project is accepted. Academic users are free to publish papers dealing with specific genes or small sets of genes. If these data are used for publication, please contact the responsible persons below to determine the acknowledgement.
Triticum turgidum
NLR-encoding genes were sequenced from 59 accessions of the tetraploid wheat Triticum turgidum as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Jonathan Jones (TSL) in collaboration with Dr. Ksenia Krasileva (University of California, Berkeley) and under the auspices of 2Blades Foundation. The data were uploaded to the European Nucleotide Archive and can be downloaded under project PRJEB34907
Restrictions on data use
You are welcome to use these data to advance your studies of the plant immune system.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a genome-wide, whole-assembly scale prior to publication by the producers (Reserved Analyses). Reserved Analyses include the identification of complete sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and comparisons with other Triticeae.
The embargo on publication of Reserved Analyses by researchers outside of the pan-NLR’ome Project is expected to extend until a first publication of the results of the project is accepted. Academic users are free to publish papers dealing with specific genes or small sets of genes. If these data are used for publication, please contact the responsible persons below to determine the acknowledgement.
Aegilops sharonensis
NLR-encoding genes were sequenced from 100 accessions of Aegilops sharonensis as part of the GBMF-funded Resistance Gene Diversity (pan-NLR’ome) project performed by the laboratory of Jonathan Jones (TSL) in collaboration with Dr. Brande Wulff (John Innes Centre) and under the auspices of 2Blades Foundation. The data were uploaded to the European Nucleotide Archive and can be downloaded under projects PRJEB35211 and PRJEB35215.
Restrictions on data use
You are welcome to use these data to advance your studies of the plant immune system.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a genome-wide, whole-assembly scale prior to publication by the producers (Reserved Analyses). Reserved Analyses include the identification of complete sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and comparisons with other Triticeae.
The embargo on publication of Reserved Analyses by researchers outside of the pan-NLR’ome Project is expected to extend until a first publication of the results of the project is accepted. Academic users are free to publish papers dealing with specific genes or small sets of genes. If these data are used for publication, please contact the responsible persons below to determine the acknowledgement.