Dataset for the ancestral sequence reconstruction of NRC3

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