Structural Variation of the Turtle Mitochondrial Control Region
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ORIGINAL ARTICLE
Structural Variation of the Turtle Mitochondrial Control Region Lucas E. Bernacki1,2 · C. William Kilpatrick2 Received: 4 July 2019 / Accepted: 5 August 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an ATrich fold (secondary structure) near the 3’ terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3’ terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription. Keywords D-loop region · Turtles (Testudines) · Mitochondrial DNA · Conserved sequence blocks · Terminationassociated sequences · TWINKLE
Introduction The mitochondrial D-loop region (or control region) is the only substantial non-coding span of DNA sequence within the mitochondrial genome of many vertebrates (Boore 1999) and is located between tRNA-Pro and tRNA-Phe in most vertebrates (Saccone et al. 1987). Sections of sequence Handling editor: Joshua Rest. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00239-020-09962-0) contains supplementary material, which is available to authorized users. * Lucas E. Bernacki [email protected] 1
Department of Sciences, Saint Joseph’s College, Mercy Hall, Rm 122, 278 Whites Bridge Road, Standish, ME 04084, USA
Department of Biology, University of Vermont, Burlington, VT, USA
2
within the mtD-loop region differ in their rate of evolution and genetic variation, with short blocks of conserved sequence that are interspersed among more variable sections. Conserved structural elements come in two forms: conserved sequence bl
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