DOI: 10.5281/zenodo.10729125
title: Dataset used in "Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector"

description: [Figs 1 and S2]

 

00_cloned_NRC123.fasta

 

FASTA file containing NRC1, NRC2 and NRC3 sequences tested in HR cell death assay.

 

01_NRCX0123_4species.fasta

 

FASTA file containing NRC0, NRC1, NRC2, NRC3 and NRCX of N. benthamiana, C. annuum (pepper), S. tuberosum (potato) and S. lycopersicum (tomato). In addition to a previously published dataset (Selvaraj et al., 2023), we included the NbNRC2, CaNRC3 and StNRC3 sequences from 00_cloned_NRC123.fasta.

 

02_NRCX0123_4species.local_aln.fasta

 

FASTA file containing the protein sequence alignment of 01_NRCX0123_4species.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).

 

03_NRCX0123_4species.local_aln.clip.fasta

 

FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used ClipKIT for trimming (Steenwyk et al., 2020).

 

04_NRCX0123_4species.local_aln.clip.fasta.treefile

 

Newick file containing the phylogenetic tree reconstructed based on 03_NRCX0123_4species.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).

 

[Fig 2B]

 

05_cloned_NRC123.local_aln.fasta

 

FASTA file containing the protein sequence alignment of 00_cloned_NRC123.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).

 

[Fig 5 and Table S1]

 

06_NRCH_cds_23-06-20.min2400max2800.fasta

 

FASTA file containing the nucleotide sequences of helper NRC sequences from 124 Solanaceae genomes (Sugihara et al., 2023; Huang et al., 2023). We filtered out sequences shorter than 2,400 or longer than 2,800 bases, resulting in 1,748 sequences.

 

07_NRCH_cds_23-06-20.min2400max2800.aa.fasta

 

FASTA file of the amino acid sequences translated from 06_NRCH_cds_23-06-20.min2400max2800.fasta.

 

08_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.fasta

 

FASTA file containing the amino acid sequences of NB-ARC module corresponding to the sequences in 07_NRCH_cds_23-06-20.min2400max2800.aa.fasta.

 

09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta

 

FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used MAFFT and ClipKIT for the alignment and trimming, respectively (Katoh & Standley, 2013; Steenwyk et al., 2020).

 

10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile

 

Newick file containing the phylogenetic tree reconstructed based on 09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).

 

11_NRCX123_cds_23-06-20.min2400max2800.fasta

 

FASTA file containing the the nucleotide sequences of NRC1/2/3X clades identified based on 10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile.

 

12_NRCX123_nt_codon_ancseq_v1.2.1.zip

 

Results of ancestral sequence reconstruction. We used ancseq to perform ancestral sequence reconsturction (Sugihara, 2024). "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta" is an input alignment and "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta.treefile" is a tree file. Regarding the output files for ancseq, please refer to the GitHub repository.

 

[Fig S7]

 

13_logo_plot.zip

 

Sequence alignments and script used in Fig S7. To generate the consensus sequence shown in Fig S7, we concatenated interfaces 1, 2 and 3 with SS15 and visualized the results using logomaker (Tareen and Kinney, 2020).

 

References

 

Huang C-Y, Huang Y-S, Sugihara Y, Wang H-Y, Huang L-T, Lopez-Agudelo JC, Chen Y-F, Lin K-Y, Chiang B-J, Toghani A, Kourelis J, Derevnina L, Wu C-H. 2023. Functional divergence shaped the network architecture of plant immune receptors. bioRxiv. 2023:2023.12.12.571219. DOI: 10.1101/2023.12.12.571219.

Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30:772–780. DOI: 10.1093/molbev/mst010.

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution 37:1530–1534. DOI: 10.1093/molbev/msaa015.

Selvaraj M, Toghani A, Pai H, Sugihara Y, Kourelis J, Yuen ELH, Ibrahim T, Zhao H, Xie R, Maqbool A, Concepcion JCD la, Banfield MJ, Derevnina L, Petre B, Lawson DM, Bozkurt TO, Wu C-H, Kamoun S, Contreras MP. 2023. Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. bioRxiv. 2023:2023.12.17.572070. DOI: 10.1101/2023.12.17.572070.

Steenwyk JL, Iii TJB, Li Y, Shen X-X, Rokas A. 2020. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology 18:e3001007. DOI: 10.1371/journal.pbio.3001007.

Sugihara Y. 2024. YuSugihara/ancseq: v1.2.1. Zenodo. DOI: 10.5281/zenodo.10808871.

Sugihara Y, Toghani A, Kamoun S, Kourelis J. 2023. NLRome dataset from 124 genomes of plants in the Solanaceae family. Zenodo. DOI: 10.5281/zenodo.10354350.

Tareen A, Kinney JB. 2020. Logomaker: beautiful sequence logos in Python. Bioinformatics 36:2272–2274. doi:10.1093/bioinformatics/btz921