Dataset for the ancestral sequence reconstruction of NRC3
Creators
- 1. The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, UK
Description
Please refer to the material_and_method.pdf to check how we generated each file.
01_NRCH_cds_23-03-03.fasta
FASTA file containing the nucleotide sequences of 2341 NRC helper sequences extracted from 124 Solanaceae NLRome dataset [1] and 20 NRC helper sequences from Adachi et al. 2023 [2].
02_NRCH_cds_23-03-03.min2400max2800.fasta
FASTA file containing the nucleotide sequences of 1753 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp.
03_NRCH_cds_23-03-03.min2400max2800.uniq.fasta
FASTA file containing the nucleotide sequences of 1116 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp and to remove duplicates.
04_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.fasta
FASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates.
05_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta
FASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates and after alignment with MAFFT.
06_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta.treefile
Newick file containing the phylogenetic tree of the 1116 NB-ARC domains of NRC helpers reconstructed with FastTree.
07_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.fasta
FASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades.
08_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.aln.fasta
FASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades after alignment with MAFFT.
09_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta
FASTA file containing the 324 full-length nucleotide sequences of the NRC1/2/3/X clades threaded onto the protein alignment with MAFFT.
10_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta.treefile
Newick file containing the phylogenetic tree of the 324 full-length nucleotide sequences of the NRC1/2/3/X clades reconstructed with IQ-TREE.
11_FastML_NRC123X.zip
Zip file containing the FastML results for the ancestral sequence reconstruction of the NRC1/2/3/X clades.
1. Sugihara, Y., Toghani, A., Kamoun, S., & Kourelis, J. (2023). NLRome dataset from 124 genomes of plants in the Solanaceae family. Zenodo. https://doi.org/10.5281/zenodo.10354350
2. Adachi, H., Sakai, T., Harant, A., Pai, H., Honda, K., Toghani, A., Claeys, J., Duggan, C., Bozkurt, T. O., Wu, C., & Kamoun, S. (2023). An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana. PLOS Genetics, 19(1), e1010500. https://doi.org/10.1371/journal.pgen.1010500
Files
material_and_method.pdf
Files
(51.4 MB)
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