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Mitogenomics Reveals a Novel Genetic Code in Hemichordata

https://doi.org/10.1093/gbe/evy254
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Transfer RNA Mutation and the Malleability of the Genetic Code
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Queuosine Modification of tRNA: A Case for Convergent Evolution
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The Phylogenetic Position of the Pterobranch Hemichordates Based on 18S rDNA Sequence Data
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Recent Evidence for Evolution of the Genetic Code
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Planarian mitochondria II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences
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Evolution of the mitochondrial genetic code I. Origin of AGR serine and stop codons in metazoan mitochondria
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Codon reassignment (codon capture) in evolution
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Codons AGA and AGG are read as glycine in ascidian mitochondria
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Complete mtDNA of Ciona intestinalis Reveals Extensive Gene Rearrangement and the Presence of an atp8 and an Extra trnM Gene in Ascidians
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The origin of the genetic code
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Unusual genetic codes and a novel gene structure for tRNASer in starfish mitochondria! DNA
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Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record
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Phylogenomic Resolution of the Hemichordate and Echinoderm Clade
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Genomics: Evolution of the Genetic Code
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Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts
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Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata
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FASconCAT: Convenient handling of data matrices
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MITOS: Improved de novo metazoan mitochondrial genome annotation
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Mitogenomics at the base of Metazoa
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Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida)
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7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNASerGCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria
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Possible anticodon sequences of tRNAHis, tRNAAsn, and tRNAAsp from Escherichia coli. Universal presence of nucleoside O in the first position of the anticodons of these transfer ribonucleic acid
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Rewiring the keyboard: evolvability of the genetic code
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Xenacoelomorpha is the sister group to Nephrozoa
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New deep-sea species of Xenoturbella and the position of Xenacoelomorpha
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Natural expansion of the genetic code
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Modern Antarctic acorn worms form tubes
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Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons
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Polyadenylation and degradation of mRNA in mammalian mitochondria: a missing link?
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Codon reassignment and amino acid composition in hemichordate mitochondria
inferredcites →https://doi.org/10.1073/pnas.97.21.11359openalex-snapshot
Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms
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A Novel Wobble Rule Found in Starfish Mitochondria
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
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Hemichordate Molecular Phylogeny Reveals a Novel Cold-Water Clade of Harrimaniid Acorn Worms
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Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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GCUA: general codon usage analysis.
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Artemis: sequence visualization and annotation
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CONSEL: for assessing the confidence of phylogenetic tree selection
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CREx: inferring genomic rearrangements based on common intervals
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/genetics/140.3.1047openalex-snapshot
Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome.
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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
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Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection
inferredcites →https://doi.org/10.1093/molbev/mss274openalex-snapshot
Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): Six Linear Chromosomes, Fragmented rRNAs, tRNA Editing, and a Novel Genetic Code
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/27.7.1683openalex-snapshot
The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria
inferredcites →https://doi.org/10.1093/nar/27.8.1767openalex-snapshot
Animal mitochondrial genomes
inferredcites →https://doi.org/10.1093/nar/gkl044openalex-snapshot
GenDecoder: genetic code prediction for metazoan mitochondria
inferredcites →https://doi.org/10.1093/nar/gkq316openalex-snapshot
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA
inferredcites →https://doi.org/10.1093/nar/gkt842openalex-snapshot
Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria
inferredcites →https://doi.org/10.1098/rstb.2007.2246openalex-snapshot
Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives
inferredcites →https://doi.org/10.1126/science.1180674openalex-snapshot
Hungry Codons Promote Frameshifting in Human Mitochondrial Ribosomes
inferredcites →https://doi.org/10.1126/science.1250691openalex-snapshot
Stop codon reassignments in the wild
inferredcites →https://doi.org/10.1128/mmbr.56.1.229-264.1992openalex-snapshot
Recent evidence for evolution of the genetic code.
inferredcites →https://doi.org/10.1128/mr.56.1.229-264.1992openalex-snapshot
Recent evidence for evolution of the genetic code
inferredcites →https://doi.org/10.1186/1471-2105-12-s9-s6openalex-snapshot
A method for computing an inventory of metazoan mitochondrial gene order rearrangements
inferredcites →https://doi.org/10.1186/1471-2148-11-134openalex-snapshot
The enigmatic mitochondrial genome of Rhabdopleura compacta(Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
inferredcites →https://doi.org/10.1186/1471-2148-9-107openalex-snapshot
The mitochondrial genome structure of Xenoturbella bocki(phylum Xenoturbellida) is ancestral within the deuterostomes
inferredcites →https://doi.org/10.1186/1471-2164-7-182openalex-snapshot
The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda)
inferredcites →https://doi.org/10.1186/1756-0500-2-192openalex-snapshot
A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis
inferredcites →https://doi.org/10.1371/journal.pbio.0040127openalex-snapshot
Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0162564openalex-snapshot
The Global Diversity of Hemichordata
inferredcites →https://doi.org/10.4061/2011/623095openalex-snapshot
tRNA Modification and Genetic Code Variations in Animal Mitochondria

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa
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Phylum Hemichordata
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Widespread use of the “ascidian” mitochondrial genetic code in tunicates
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Putative Ordovician green alga Krejciella reinterpreted as enteropneust hemichordate tube (Czech Republic)
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Highly rearranged gene orders and rapid evolutionary rates in the mitochondrial genomes of Apodida (Echinodermata: Holothuroidea)
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Unraveling the phylogeny of Chaetopteridae (Annelida) through mitochondrial genome analysis
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The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes
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Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence
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Additional file 1 of The embryology, metamorphosis, and muscle development of Schizocardium karankawa sp. nov. (Enteropneusta) from the Gulf of Mexico
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A computational screen for alternative genetic codes in over 250,000 genomes
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