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Background  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 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.    Results  We 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: tRNA Arg , 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 tRNA Arg  gene appears to have been converted to a tRNA Gln  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 tRNA Leu  genes, as well as a translocation of the tRNA Ala  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 tRNA Glu  gene from its original position.  Uroplatus fimbriatus  appears to retain a translocated tRNA Glu  gene adjacent to the 5’ end of the major noncoding region.    Conclusions  The 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 material  The online version of this article (doi:10.1186/1471-2164-15-930) contains supplementary material, which is available to authorized users.

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