The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA

Parham, James F.; Feldman, Chris R.; Boore, Jeffrey L.

doi:10.1186/1471-2148-6-11

The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA

Journal Article · Mon Feb 06 23:00:00 EST 2006 · BMC Evolutionary Biology (Online)

DOI:https://doi.org/10.1186/1471-2148-6-11· OSTI ID:1626373

Parham, James F. ^[1]; Feldman, Chris R. ^[2]; Boore, Jeffrey L. ^[3]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Evolutionary Genomics; Univ. of California, Berkeley, CA (United States). Museum of Palentology; DOE/OSTI
Utah State Univ., Logan, UT (United States). Dept. of Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Evolutionary Genomics; Univ. of California, Berkeley, CA (United States). Dept. of Integrative Biology

Background: The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis. Results: We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles. Conclusion: Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626373

Journal Information:: BMC Evolutionary Biology (Online), Journal Name: BMC Evolutionary Biology (Online) Journal Issue: 1 Vol. 6; ISSN 1471-2148

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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