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Comment
. 2023 Feb;614(7948):E33-E36.
doi: 10.1038/s41586-022-05634-9.

Reply to: The case for standardizing gene nomenclature in vertebrates

Constantina Theofanopoulou  1   2 , Erich D Jarvis  3   4   5
Affiliations
Comment

Reply to: The case for standardizing gene nomenclature in vertebrates

Constantina Theofanopoulou et al. Nature. 2023 Feb.
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Family tree for genes that encode the oxytocin and vasopressin receptors.
Tree topology inferred with the phylogenetic maximum likelihood method on an exon nucleotide alignment (MAFFT), with 1,000 non-parametric bootstrap replicates (IQ-TREE). Bootstrap values are shown as percentages at the branch points. The tree is rooted with the VTR gene in amphioxus. The gene names of the current accessions (see Table 1 in Theofanopoulou et al. and Supplementary Tables 4a–e in Theofanopoulou et al. for a full list of synonyms) were written over according to our revised synteny- and phylogeny-based orthology. All sequences used, FASTA alignment and Newick tree files can be accessed here at https://github.com/constantinatheo/universalnomenclature/. Scale bar, 0.62 substitutions. For a discussion on interchanging VTR2A and VTR2C naming, see Supplementary Note 3.
Extended Data Fig. 1
Extended Data Fig. 1. Checklist and caveats.
Suggested checklist and caveats to be considered for synteny (top) and phylogeny (bottom) evidence used to propose gene nomenclature.
See this image and copyright information in PMC

Comment on

References

    1. McCarthy FM, et al. The case for standardizing gene nomenclature in vertebrates. Nature. 2022 doi: 10.1038/s41586-022-05633-w. - DOI - PMC - PubMed
    1. Theofanopoulou C, Gedman G, Cahill JA, Boeckx C, Jarvis ED. Universal nomenclature for oxytocin–vasotocin ligand and receptor families. Nature. 2021;592:747–755. doi: 10.1038/s41586-020-03040-7. - DOI - PMC - PubMed
    1. Jarvis ED, et al. Avian brains and a new understanding of vertebrate brain evolution. Nat. Rev. Neurosci. 2005;6:151–159. doi: 10.1038/nrn1606. - DOI - PMC - PubMed
    1. Theofanopoulou C. Reconstructing the evolutionary history of the oxytocin and vasotocin receptor gene family: Insights on whole genome duplication scenarios. Dev. Biol. 2021;479:99–106. doi: 10.1016/j.ydbio.2021.07.012. - DOI - PubMed
    1. Wain HM, et al. Guidelines for human gene nomenclature. Genomics. 2002;79:464–470. doi: 10.1006/geno.2002.6748. - DOI - PubMed