Dataset Information

Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.

ABSTRACT: A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker's snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria.

SUBMITTER: Russell RD

PROVIDER: S-EPMC2706983 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

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Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.

Russell R David RD Beckenbach Andrew T AT

Journal of molecular evolution 20081201 6

A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we ...[more]

PMID: 19030769

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Project description:The Kemp's ridley (Lepidochelys kempii) is the world's most endangered sea turtle species and is primarily distributed in the Gulf of Mexico. In the United States, South Padre Island, Texas serves as a key nesting ground for the species. Genetic studies of the Kemp's ridley have been used to aid in conservation and management practices, with the mitochondrial control region as the most commonly used marker due to its perceived hypervariability and ease of sequencing. However, with the advent of next generation sequencing technology, targeting complete mitochondrial genomes is now feasible. Here, we describe a more complete mitochondrial genome for the Kemp's ridley than has been previously published in literature and demonstrate a cost-effective and efficient method for obtaining complete mitochondrial genomes from sea turtles. We compare the genetic diversity and taxonomic resolution obtained from whole mitochondrial genomes to that obtained from the mitochondrial control region alone. We compare current genetic diversity with previous records. Furthermore, we evaluate the genetic structure between the breeding stock in South Padre Island and that of deceased Kemp's ridleys recovered on the Northern coast of the Gulf of Mexico after the 2010 BP Deepwater Horizon oil spill, and of Kemp's ridleys stranded on the East Coast of the United States. Our results show that complete mitochondrial genomes provide greater resolution than the control region alone. They also show that the genetic diversity of the Kemp's ridley has remained stable, despite large population declines, and that the genetic makeup of deceased turtles stranded after the Deepwater Horizon oil spill is indistinguishable from the breeding stock in South Padre Island, Texas. Open Data Badge:This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/genbank/.

Dataset Information

Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.

Publications

Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.

Similar Datasets

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