We report a section-wide NLRome for the tuber-bearing section Petota of Solanum, containing the most important non-cereal food crop, potato. Evolutionary and comparative genomic and functional analyses empower the discovery of new genes showing borad-spectrum resistance against late blight. These results will accelerate resistance introgression and/or stacking in hybrid potato breeding and our methodology also enlightens how NLRome discovers the knowns from the known unknowns of resistance gene repertoire in other crop species.
Please cite:
Li, N., He, Q., Wang, J. et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet 55, 852–860 (2023). https://doi.org/10.1038/s41588-023-01340-y
Pipelines and relevant scripts for:
- Genome assembly and assessment
- Genome annotation
- Phylogenetic analyses
- NLR reaannotation and curation
- Construction and analyses of the NLRome
- Identification and analyses of integrated domains
- Effector-based GWAS
- NLR synteny plot
- Clades12 34 NLR clade comparison
Important
- Versions of all required software are stated in the "Methods" section of the manuscript
- There is no need to install these scripts; just download them and make necessary modifications
- All instructions/demo to run these pipelines are presented in the work.sh or *.sh files in each directory using shell programing language
MIT
Hongbo Li (lihongbo_solab@163.com)
Luyao Wang (wangluyao@caas.cn)
Suomeng Dong (smdong@njau.edu.cn)
Sanwen Huang (huangsanwen@caas.cn)