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6 results for “Ancestral Sequence Reconstruction”
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> </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> </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> </p><p>1. Sugihara, Y., Toghani, A., Kamoun, S., & 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., & 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> </p>
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
<p>Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.</p>
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
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ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability
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Data from: Elucidating the functional evolution of heat sensors among Xenopus species adapted to different thermal niches by ancestral sequence reconstruction
Ambient temperature fluctuations are detected via the thermosensory system which allows animals to seek preferable thermal conditions or escape from harmful temperatures. Evolutionary changes in thermal perception have thus potentially played crucial roles in niche selection. The genus Xenopus (clawed frog) is suitable for investigating the relationship between thermal perception and niche selection due to their diverse latitudinal and altitudinal distributions. Here we performed comparative analyses of the neuronal heat sensors TRPV1 and TRPA1 among closely related Xenopus species (X. borealis, X. muelleri, X. laevis, and X. tropicalis) to elucidate their functional evolution and to assess whether their functional differences correlate with thermal niche selection among the species. Comparison of TRPV1 among four extant Xenopus species and reconstruction of the ancestral TRPV1 revealed that TRPV1 responses to repeated heat stimulation were specifically altered in the lineage leading to X. tropicalis which inhabits warmer niches. Moreover, the thermal sensitivity of TRPA1 was lower in X. tropicalis than the other species, although the thermal sensitivity of TRPV1 and TRPA1 was not always lower in species that inhabit warmer niches than the species inhabit cooler niches. However, a clear correlation was found in species differences in TRPA1 activity. Heat-evoked activity of TRPA1 in X. borealis and X. laevis, which are adapted to cooler niches, was significantly higher than in X. tropicalis and X. muelleri which are adapted to warmer niches. These findings suggest that the functional properties of heat sensors changed during Xenopus evolution, potentially altering the preferred temperature ranges among species.
Data from: Elucidating the functional evolution of heat sensors among Xenopus species adapted to different thermal niches by ancestral sequence reconstruction
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