Dataset for the ancestral sequence reconstruction of NRC3 Article Swipe
Yu Sugihara
,
AmirAli Toghani
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10360198
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10360198
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
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Metadata
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- Language
- en
- Landing Page
- https://doi.org/10.5281/zenodo.10360198
- OA Status
- green
- Cited By
- 1
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4393417926Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.5281/zenodo.10360198Digital Object Identifier
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Dataset for the ancestral sequence reconstruction of NRC3Work title
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datasetOpenAlex work type
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enPrimary language
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2023Year of publication
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2023-12-12Full publication date if available
- Authors
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Yu Sugihara, AmirAli ToghaniList of authors in order
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https://doi.org/10.5281/zenodo.10360198Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://doi.org/10.5281/zenodo.10360198Direct OA link when available
- Concepts
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Sequence (biology), Evolutionary biology, Computer science, Computational biology, Biology, GeneticsTop concepts (fields/topics) attached by OpenAlex
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1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.full-length | 179, 193, 211, 235 |
| abstract_inverted_index.benthamiana. | 323 |
| abstract_inverted_index.phylogenetic | 160, 230 |
| abstract_inverted_index.reconstructed | 170, 242 |
| abstract_inverted_index.reconstruction | 256 |
| abstract_inverted_index.11_FastML_NRC123X.zip | 245 |
| abstract_inverted_index.material_and_method.pdf | 4 |
| abstract_inverted_index.01_NRCH_cds_23-03-03.fasta | 12 |
| abstract_inverted_index.https://doi.org/10.5281/zenodo.10354350 | 284 |
| abstract_inverted_index.02_NRCH_cds_23-03-03.min2400max2800.fasta | 42 |
| abstract_inverted_index.https://doi.org/10.1371/journal.pgen.1010500 | 328 |
| abstract_inverted_index.03_NRCH_cds_23-03-03.min2400max2800.uniq.fasta | 64 |
| abstract_inverted_index.07_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.fasta | 173 |
| abstract_inverted_index.04_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.fasta | 90 |
| abstract_inverted_index.08_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.aln.fasta | 187 |
| abstract_inverted_index.09_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta | 205 |
| abstract_inverted_index.05_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta | 120 |
| abstract_inverted_index.10_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta.treefile | 225 |
| abstract_inverted_index.06_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta.treefile | 155 |
| cited_by_percentile_year | |
| countries_distinct_count | 1 |
| institutions_distinct_count | 2 |
| citation_normalized_percentile |