Evolutionary Dynamics of ADAR/ADAD Genes

Protein sequences of Nematostella vectensis (GenBank: XP_001642062.2, XP_001629615.2), Drosophila melanogaster (GenBank: NP_569940.2), Caenorhabditis elegans (GenBank: NP_492153.2, NP_498594.1), Crassostrea gigas (GenBank: EKC20855.1, EKC32699.1, XP_011441313.2), Strongylocentrotus purpuratus (GenBank: XP_011680614.1, XP_781832.1, XP_030847369.1), Ciona intestinalis (GenBank: XP_002128212.1), Danio rerio (GenBank: NP_571671.2, NP_571685.2, XP_021334693.1, XP_686426.5, NP_001277142.1, XP_687183.1) and Homo sapiens (GenBank: XP_024305442.1, NP_056648.1, NP_061172.1, NP_640336.1, NP_631913.3) collected from NCBI were used as queries to search for ADAR/ADAD genes in the public reference genome and the de novo transcriptome assemblies (assembled by Trinity⁹² (link)) of the 22 species by TBLASTN⁹³ (link) with parameters -F F -e 1e-5, followed by the determination of protein sequences in the target species with GeneWise.⁹⁴ (link) The predicted proteins were then aligned to the NCBI nr database to confirm whether they were ADARs/ADADs. Domain organizations of the manually confirmed ADAR/ADAD proteins were predicted using the CD-Search tool in NCBI (CDD)⁹⁵ (link) and Pfam⁹⁶ (link) with default settings.
Phylogenetic analysis of ADARs and ADADs identified above, were performed with the adenosine-deaminase (AD) domains (around 324 amino acids in length; see Table S2 for the sequences) using RAxML⁹⁷ (link) with the Maximum Likelihood (ML) method (parameter: -m PROTGAMMAIJTT) and using Mrbayes⁹⁸ (link) with Bayesian Inference (BI) method (parameters: prset aamodelpr = fixed(Wag); lset rates = invgamma; mcmcp ngen = 1000000 nchains = 4 samplefreq = 100 burnin = 200), respectively. The AD peptide sequences used for phylogenetic analysis were aligned using PRANK.⁹⁹ (link) Reliability of the ML tree was estimated based on 1,000 bootstrap replications. The structures of phylogenetic trees generated by the two methods were generally consistent with each other (Figure S2). The information of ADAR genes annotated in each species, including the coding nucleotide sequences, protein sequences, domain annotations are presented in Table S2.

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Zhang P., Zhu Y., Guo Q., Li J., Zhan X., Yu H., Xie N., Tan H., Lundholm N., Garcia-Cuetos L., Martin M.D., Subirats M.A., Su Y.H., Ruiz-Trillo I., Martindale M.Q., Yu J.K., Gilbert M.T., Zhang G, & Li Q. (2023). On the origin and evolution of RNA editing in metazoans. Cell Reports, 42(2), 112112.

Publication 2023

Adenosine deaminase Amino acids Caenorhabditis elegans Ciona intestinalis Coding nucleotide sequences Crassostrea gigas Danio rerio Drosophila melanogaster Genes Genome Homo sapiens Peptide Protein sequences Protein sequences determination Proteins Proteins domain Replications Strongylocentrotus purpuratus Transcriptome Trees

Corresponding Organization : Women's Hospital, School of Medicine, Zhejiang University

Other organizations : Natural History Museum Aarhus, Evolutionary Genomics (United States), University of California, Berkeley, Norwegian University of Science and Technology, Institut de Biologia Evolutiva, Institute of Cellular and Organismic Biology, Academia Sinica, Institució Catalana de Recerca i Estudis Avançats, Universitat de Barcelona, Whitney Museum of American Art, University of Florida

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Variable analysis

independent variables

Protein sequences of Nematostella vectensis, Drosophila melanogaster, Caenorhabditis elegans, Crassostrea gigas, Strongylocentrotus purpuratus, Ciona intestinalis, Danio rerio and Homo sapiens collected from NCBI

dependent variables

ADAR/ADAD genes in the public reference genome and the de novo transcriptome assemblies of the 22 species

control variables

TBLASTN parameters: -F F -e 1e-5
GeneWise used to determine protein sequences in target species
CD-Search tool in NCBI (CDD) and Pfam used to predict domain organizations of the manually confirmed ADAR/ADAD proteins
RAxML with Maximum Likelihood (ML) method (parameter: -m PROTGAMMAIJTT) and Mrbayes with Bayesian Inference (BI) method (parameters: prset aamodelpr = fixed(Wag); lset rates = invgamma; mcmcp ngen = 1000000 nchains = 4 samplefreq = 100 burnin = 200) used for phylogenetic analysis
PRANK used for alignment of AD peptide sequences

Annotations

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