Dataset and Scripts for: RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs (v.20200528_415)

RefPlantNLR v.20200528_415

See bioRxiv 2020.07.08.193961; doi: https://doi.org/10.1101/2020.07.08.193961

SUPPLEMENTAL DATA

Table S1: Description of RefPlantNLR.

Table S2: Plant orders represented in RefPlantNLR.

Supplemental dataset 1: Amino acid sequences of RefPlantNLR entries (fasta format). This file contains 415 amino acid sequences.

Supplemental dataset 2: CDS sequences of RefPlantNLR entries (fasta format). This file contains 400 CDS sequences. CDS sequences could not be retrieved for 15 RefPlantNLR entries.

Supplemental dataset 3: Annotated genomic sequences of RefPlantNLR entries (GenBank flat file format). This file contains 329 genomic loci containing the gene models of 344 RefPlantNLR entries and 56 RefPlantNLR mRNA entries lacking genomic information.

Supplemental dataset 4: InterProScan annotation of the RefPlantNLR amino acid sequences (GFF3 format). This file contains the InterProScan annotation of 415 amino acid sequences.

Supplemental dataset 5: InterProScan annotation of the RefPlantNLR CDS sequences (GFF3 format). This file contains the InterProScan annotation of the 400 CDS sequences.

Supplemental dataset 6: Amino acid sequences of the extracted RefPlantNLR NB-ARC domains (fasta format). This file contains 424 NB-ARC domain (SUPERFAMILY signature SSF52540) amino acid sequences belonging to 415 RefPlantNLR entries.

Supplemental dataset 7: Amino acid sequences of the unique RefPlantNLR extracted NB-ARC domains (fasta format). This file contains 347 unique NB-ARC domain (SUPERFAMILY signature SSF52540) amino acid sequences.

Supplemental dataset 8: Clustal Omega alignment of the unique RefPlantNLR extracted NB-ARC domains (PHYLIP format). This file contains the Clustal Omega alignment of 346 unique NB-ARC domains (SUPERFAMILY signature SSF52540) with all positions with less than 95% coverage removed. Pb1 was omitted from this alignment.

Supplemental dataset 9: NB-ARC domain phylogeny of the RefPlantNLR entries using the Maximum likelihood method (Newick format). This file contains the phylogenetic analysis of the NB-ARC domain of the RefPlantNLR entries using the JTT method.

Supplemental dataset 10: Amino acid sequences of the non-redundant RefPlantNLR entries (fasta format). This file contains 235 amino acid sequences representing the non-redundant RefPlantNLR entries at a 90% amino acid identity threshold per genus according to the NB-ARC domain.

Supplemental dataset 11: Amino acid sequences of the NB-ARC domains of the non-redundant RefPlantNLR entries (fasta format). This file contains 241 amino acid sequences representing the extracted NB-ARC domains of the 235 non-redundant RefPlantNLR.

Appendix S1: R script used to generate annotations and figures.

Appendix S2: InterProScan descriptions used for generating annotations.