PotatoNLRome

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

:label: Content

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

:wine_glass: License

MIT

:email: Contacts

Hongbo Li (lihongbo_solab@163.com)

Luyao Wang (wangluyao@caas.cn)

Suomeng Dong (smdong@njau.edu.cn)

Sanwen Huang (huangsanwen@caas.cn)