Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes.

Yoshinori Kumazawa,Saaya Miura,Yasuyuki Hashiguchi,Chiemi Yamada

doi:10.1186/1471-2164-15-930

Abstract

BackgroundVertebrate mitochondrial genomes (mitogenomes) are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study.ResultsWe determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5’ end of the major noncoding region.ConclusionsThe present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-930) contains supplementary material, which is available to authorized users.

Highlights

IntroductionVertebrate mitochondrial genomes (mitogenomes) are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes
Vertebrate mitochondrial genomes are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes
Together with the information derived from T. tripolitanus and T. steudneri (Figure 1), these results suggest that the gene rearrangement found in S. petrii, in which tRNAAla and OL are translocated to the 5’ end of WNCY genes (Figure 1C), is not widely distributed among Tropiocolotes and Stenodactylus geckos

Summary

Introduction

Vertebrate mitochondrial genomes (mitogenomes) are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution gene rearrangements have been described for diverse lineages. Metazoan mitochondrial genomes (mitogenomes) are double-stranded circular DNAs typically 16–18 kbp in size (reviewed in [1,2,3]). The typical vertebrate gene organization (Figure 1A), which was first revealed for the human mitogenome [4], is shared by many species of fishes, amphibians, reptiles, and mammals. Gene inversions are quite rare in vertebrate mitogenomes though not unknown [10]

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