{
  "abstract": "Background: The dihydrouridine arm (D-arm) is a conserved structural element of canonical transfer RNAs (tRNAs) and contributes to the characteristic L-shaped tertiary structure, required for ribosomal interaction. In mitochondrial tRNAs (mt-tRNAs), however, structural constraints are relaxed, and loss of the D-arm has been observed in several metazoan phylogenies, indicating that alternative stabilisation mechanisms may compensate for its absence. In snakes (Serpentes)—a species-rich reptile order with highly derived mitochondrial genomes—it has not been systematically investigated whether this structural simplification has occurred. Building on our recent description of complete D-arm loss in the mitochondrial tRNA-Cys of Macrovipera lebetinus lebetinus , we present the first comparative analysis of this structural feature in Serpentes.\n\nResults: A total of 136 serpent mitogenomes and two lizard outgroups ( Anolis carolinensis , D-arm present; Pogona vitticeps , D-arm lost) were analysed using tRNAscan-SE 2.0.12 with the vertebrate mitochondrial model. Loss of the D-arm was detected in 20 sequences (14.7%). This modification was observed in all sampled Viperinae (8/8), Xenodermidae (3/3), Acrochordidae (1/1), and Tropidophiidae (1/1), and partially prevalent in Pythonidae (2/4, 50%), Elapidae (2/13, 15.4%), and Crotalinae (2/31, 6.5%), with a single case in Colubridae (1/58, 1.7%). Maximum parsimony reconstruction required nine changes of state, corresponding to seven to nine independent loss events; stochastic character mapping gave a mean of 9.14 ( 95% CI: 8-11). Cysteine codon usage showed no significant association with D-arm loss (t-test: p = 0.755; Mann-Whitney U test: p = 0.837). D-arm loss was, however, associated with a significantly shorter TΨC-arm stem (phylANOVA: p = 0.029), unlike the compensatory T-arm elongation described for human tRNA-Ser. A sensitivity analysis of five sequences with discordant annotations indicates five or six independent losses under alternative annotations.\n\nConclusions: Predicted D-arm loss in mitochondrial tRNA-Cys is a recurring, independently evolved, structural reduction in Serpentes. No association with codon usage was detected, either before or after phylogenetic correction (phylANOVA: p = 0.883), whereas TΨC-arm stem length differed significantly, suggesting a distinct mode of structural accommodation from that reported for tRNA-Ser. These results highlight the structural plasticity of mitochondrial tRNA in reptiles and raise questions about the compensatory molecular mechanisms—including possible mitochondrial-nuclear coevolution—that enable functional tRNA activity even in the absence of a canonical structural element.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "name": "Stephan Siegert"
    },
    {
      "name": "Joel Fonseca Nogueira",
      "orcid": "0000-0002-1425-2036"
    },
    {
      "name": "Daniel Jestrzemski"
    },
    {
      "name": "Mike Reich",
      "orcid": "0000-0003-3837-3497"
    },
    {
      "name": "Bertram Brenig"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3td28w5xjs0n9.bib",
  "cited_by": 0,
  "doi": "10.1186/s12864-026-13478-0",
  "fulltext_url": null,
  "id": "3td28w5xjs0n9",
  "issns": [
    "1471-2164"
  ],
  "landing_url": "https://link.springer.com/article/10.1186/s12864-026-13478-0",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [],
  "openalex": null,
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-31",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/3td28w5xjs0n9.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T00:20:55Z",
      "native_id": "10.1186/s12864-026-13478-0",
      "source": "crossref",
      "url": "https://link.springer.com/article/10.1186/s12864-026-13478-0"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "issn:1471-2164",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Convergent loss of the D-arm in mitochondrial tRNA-Cys across sampled Serpentes mitogenomes: a systematic comparative analysis",
  "title_text": "Convergent loss of the D-arm in mitochondrial tRNA-Cys across sampled Serpentes mitogenomes: a systematic comparative analysis",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T00:21:39Z",
  "url": "https://research.draconitic.com/paper/3td28w5xjs0n9",
  "venue": "BMC Genomics",
  "versions": []
}