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Data for Dynamic evolution of the MutS family in animals: multiple losses of MSH paralogues and gain of a viral MutS homologue in octocorals

https://doi.org/10.17605/osf.io/rn9ft
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Mechanisms of DNA damage, repair, and mutagenesis
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Characterization of mitochondrial proteomes of nonbilaterian animals
inferredcites →https://doi.org/10.1007/pl00006321openalex-snapshot
Mitochondrial DNA of the coral sarcophyton glaucum contains a gene for a homologue of bacterial muts: A possible case of gene transfer from the nucleus to the mitochondrion
inferredcites →https://doi.org/10.1007/pl00006429openalex-snapshot
Sequence Analysis of the Mitochondrial Genome of Sarcophyton glaucum: Conserved Gene Order Among Octocorals
inferredcites →https://doi.org/10.1007/s00338-011-0864-xopenalex-snapshot
Description of viral assemblages associated with the Gorgonia ventalina holobiont
inferredcites →https://doi.org/10.1007/s004380000370openalex-snapshot
Functional analysis of the Bacillus subtilis yshD gene, a mutS paralogue
inferredcites →https://doi.org/10.1016/b978-0-444-82235-2.50029-1openalex-snapshot
Mitochondrial Genomes of Anthozoa (Cnidaria)
inferredcites →https://doi.org/10.1016/j.dnarep.2004.10.002openalex-snapshot
The yeast MSH1 gene is not involved in DNA repair or recombination during meiosis
inferredcites →https://doi.org/10.1016/j.jmb.2018.01.013openalex-snapshot
EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures
inferredcites →https://doi.org/10.1016/j.mad.2008.02.012openalex-snapshot
DNA mismatch repair: Molecular mechanism, cancer, and ageing
inferredcites →https://doi.org/10.1016/j.mrrev.2017.07.001openalex-snapshot
DNA mismatch repair and its many roles in eukaryotic cells
inferredcites →https://doi.org/10.1016/j.str.2013.08.005openalex-snapshot
High-Resolution Comparative Modeling with RosettaCM
inferredcites →https://doi.org/10.1016/j.tig.2005.11.007openalex-snapshot
Bacteriophage origins of mitochondrial replication and transcription proteins
inferredcites →https://doi.org/10.1016/j.ympev.2012.08.023openalex-snapshot
MITOS: Improved de novo metazoan mitochondrial genome annotation
inferredcites →https://doi.org/10.1016/s0021-9258(18)43978-6openalex-snapshot
Purification and characterization of MSH1, a yeast mitochondrial protein that binds to DNA mismatches.
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0960-9822(02)01187-9openalex-snapshot
The Closest Unicellular Relatives of Animals
inferredcites →https://doi.org/10.1038/35037509openalex-snapshot
Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA
inferredcites →https://doi.org/10.1038/35037523openalex-snapshot
The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatch
inferredcites →https://doi.org/10.1038/cr.2007.115openalex-snapshot
Mechanisms and functions of DNA mismatch repair
inferredcites →https://doi.org/10.1038/ismej.2010.210openalex-snapshot
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
inferredcites →https://doi.org/10.1038/ng0796-336openalex-snapshot
Involvement of mouse Mlh1 in DNA mismatch repair and meiotic crossing over
inferredcites →https://doi.org/10.1038/nm1097-1076openalex-snapshot
Gastrogenomic delights: A movable feast
inferredcites →https://doi.org/10.1038/nprot.2007.131openalex-snapshot
Locating proteins in the cell using TargetP, SignalP and related tools
inferredcites →https://doi.org/10.1038/nsmb.2175openalex-snapshot
Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops
inferredcites →https://doi.org/10.1038/s41559-020-1129-2openalex-snapshot
Widespread patterns of gene loss in the evolution of the animal kingdom
inferredcites →https://doi.org/10.1073/pnas.121183298openalex-snapshot
In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair
inferredcites →https://doi.org/10.1073/pnas.2001998117openalex-snapshot
MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes
inferredcites →https://doi.org/10.1073/pnas.76.4.1967openalex-snapshot
Rapid evolution of animal mitochondrial DNA.
inferredcites →https://doi.org/10.1073/pnas.92.22.10418openalex-snapshot
Mutations in the MSH3 gene preferentially lead to deletions within tracts of simple repetitive DNA in Saccharomyces cerevisiae.
inferredcites →https://doi.org/10.1074/mcp.m114.043083openalex-snapshot
MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites*
inferredcites →https://doi.org/10.1083/jcb.150.2.f31openalex-snapshot
DNA Repair in Drosophila
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv362openalex-snapshot
IBS: an illustrator for the presentation and visualization of biological sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btz512openalex-snapshot
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
inferredcites →https://doi.org/10.1093/gbe/evw195openalex-snapshot
Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/26.18.4291openalex-snapshot
A phylogenomic study of the MutS family of proteins
inferredcites →https://doi.org/10.1093/nar/28.2.463openalex-snapshot
Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins
inferredcites →https://doi.org/10.1093/nar/gkm921openalex-snapshot
The origins and early evolution of DNA mismatch repair genes—multiple horizontal gene transfers and co-evolution
inferredcites →https://doi.org/10.1093/nar/gku316openalex-snapshot
Deciphering key features in protein structures with the new ENDscript server
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
inferredcites →https://doi.org/10.1093/nar/gky448openalex-snapshot
HMMER web server: 2018 update
inferredcites →https://doi.org/10.1101/gad.13.5.523openalex-snapshot
Mouse MutS-like protein Msh5 is required for proper chromosome synapsis in male and female meiosis
inferredcites →https://doi.org/10.1111/mec.14558openalex-snapshot
The joint evolution of the Myxozoa and their alternate hosts: A cnidarian recipe for success and vast biodiversity
inferredcites →https://doi.org/10.1126/science.2665076openalex-snapshot
DNA Mismatch Correction in a Defined System
inferredcites →https://doi.org/10.1126/science.8128251openalex-snapshot
Mutation of a mutL Homolog in Hereditary Colon Cancer
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2148-11-228openalex-snapshot
A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function
inferredcites →https://doi.org/10.1186/s12862-018-1142-0openalex-snapshot
Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits
inferredcites →https://doi.org/10.1186/s13059-019-1727-yopenalex-snapshot
Performance of neural network basecalling tools for Oxford Nanopore sequencing
inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot
OrthoFinder: phylogenetic orthology inference for comparative genomics
inferredcites →https://doi.org/10.1186/s40168-018-0420-9openalex-snapshot
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
inferredcites →https://doi.org/10.1186/s40168-018-0431-6openalex-snapshot
Host-microbe interactions in octocoral holobionts - recent advances and perspectives
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pgen.1003920openalex-snapshot
Different Roles of Eukaryotic MutS and MutL Complexes in Repair of Small Insertion and Deletion Loops in Yeast
inferredcites →https://doi.org/10.1371/journal.pone.0139068openalex-snapshot
Phylogenomic Analyses Support Traditional Relationships within Cnidaria
inferredcites →https://doi.org/10.1534/genetics.109.103796openalex-snapshot
Evidence That Msh1p Plays Multiple Roles in Mitochondrial Base Excision Repair
inferredcites →https://doi.org/10.1534/genetics.116.186759openalex-snapshot
DNA Repair in Drosophila : Mutagens, Models, and Missing Genes
inferredcites →https://doi.org/10.3389/fmars.2016.00023openalex-snapshot
Comparative Metagenomics of Viral Assemblages Inhabiting Four Phyla of Marine Invertebrates
inferredcites →https://doi.org/10.4061/2010/260512openalex-snapshot
DNA Mismatch Repair in Eukaryotes and Bacteria
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