Snakes Lose Mitochondrial tRNA D-Arm in Convergent Evolution

Researchers have identified a recurring structural simplification in the mitochondrial genomes of snakes, specifically involving the loss of the D-arm in the transfer RNA for cysteine (tRNA-Cys). This finding, detailed in a systematic comparative analysis published in BMC Genomics, represents the first comprehensive investigation of this specific structural feature across the order Serpentes.

The D-arm, or dihydrouridine arm, is a conserved structural element in canonical transfer RNAs that contributes to the characteristic L-shaped tertiary structure required for ribosomal interaction. In mitochondrial tRNAs, however, structural constraints are often relaxed compared to their nuclear counterparts. The loss of the D-arm has been observed in several metazoan phylogenies, suggesting that alternative stabilization mechanisms may compensate for its absence. Despite this known plasticity, it had not been systematically investigated whether this structural reduction had occurred across the diverse and species-rich reptile order of snakes, which possess highly derived mitochondrial genomes.

To address this gap, the research team analyzed a total of 136 serpent mitogenomes along with two lizard outgroups. The outgroups, Anolis carolinensis and Pogona vitticeps, served as comparative references, with the former retaining the D-arm and the latter exhibiting its loss. The analysis utilized the tRNAscan-SE 2.0.12 software with the vertebrate mitochondrial model to detect structural features within the mitochondrial sequences.

The results revealed that loss of the D-arm was detected in 20 of the analyzed sequences, representing 14.7% of the total sample. This modification was not uniformly distributed across all snake families. It was observed in all sampled members of the subfamily Viperinae (8/8), the families Xenodermidae (3/3), Acrochordidae (1/1), and Tropidophiidae (1/1). In contrast, the prevalence was partial in other groups, including Pythonidae (2/4, 50%), Elapidae (2/13, 15.4%), and Crotalinae (2/31, 6.5%). Only a single case was identified in the large family Colubridae (1/58, 1.7%), indicating that while the loss is a notable feature, it is not universal across all sampled snake lineages.

Phylogenetic analysis was employed to understand the evolutionary history of this structural change. Maximum parsimony reconstruction required nine changes of state, corresponding to seven to nine independent loss events. Stochastic character mapping provided a mean estimate of 9.14 independent losses, with a 95% confidence interval ranging from 8 to 11. These findings suggest that the loss of the D-arm is a recurring event that has evolved independently multiple times within the snake lineage, rather than being a single ancestral trait inherited by all affected species.

The study also investigated potential functional correlates of this structural loss, specifically examining whether it was associated with changes in codon usage. Cysteine codon usage showed no significant association with D-arm loss, as indicated by a t-test (p = 0.755) and a Mann-Whitney U test (p = 0.837). Furthermore, phylogenetic correction using phylANOVA also yielded no significant association (p = 0.883).

In contrast to codon usage, the study found a significant association between D-arm loss and the length of the TΨC-arm stem. A phylANOVA test revealed that sequences lacking the D-arm had a significantly shorter TΨC-arm stem (p = 0.029). This finding is distinct from the compensatory T-arm elongation described for human tRNA-Ser, suggesting a different mode of structural accommodation in snakes. The shortening of the TΨC-arm stem may serve as a compensatory mechanism to maintain the overall structural integrity and function of the tRNA molecule in the absence of the D-arm.

A sensitivity analysis was conducted to assess the robustness of the findings, focusing on five sequences with discordant annotations. This analysis indicated that five or six independent losses would be identified under alternative annotations, supporting the conclusion that the observed losses are not artifacts of annotation errors. The study concludes that predicted D-arm loss in mitochondrial tRNA-Cys is a recurring, independently evolved structural reduction in Serpentes. 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.

Subject of Research: Comparative analysis of D-arm loss in mitochondrial tRNA-Cys across Serpentes mitogenomes

Article Title: Convergent loss of the D-arm in mitochondrial tRNA-Cys across sampled Serpentes mitogenomes: a systematic comparative analysis

Article References: Siegert, S., Fonseca Nogueira, J., Jestrzemski, D., Reich, M., & Brenig, B. (2026). Convergent loss of the D-arm in mitochondrial tRNA-Cys across sampled Serpentes mitogenomes: a systematic comparative analysis. BMC Genomics. https://doi.org/10.1186/s12864-026-13478-0

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13478-0

Keywords: mitochondrial genomics, tRNA structure, Serpentes, convergent evolution, D-arm loss, comparative analysis, phylogenetics, structural plasticity, Convergent, loss, D-arm, mitochondrial