Tandem Duplication-random Loss Research Articles

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication.

Simple SummaryHeptageniidae is one of the most abundant and widespread families of mayflies, with more than 600 described species and distributed mainly in the Holoarctic, Oriental, and Afrotropical regions. Previous phylogenetic analyses in this family mainly focused on morphological characters and were restricted to one or several genes. Ten complete mitochondrial genomes from this family are reported here. A conserved intergenic spacer and tRNA gene duplication in Heptageniidae mitogenomes may be regarded as ancient features and provide evidence for the phylogenic analysis within Ephemeroptera.Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae)

The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I′-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).

Novel tRNA gene rearrangements in the mitochondrial genome of Camarochiloides weiweii (Hemiptera: Pachynomidae)

Pachynomidae is a poorly known heteropteran group currently considered as a distinct family closely related to Reduviidae. Taxonomic position of Pachynomidae has been debated for a long time. Knowledge about mitochondrial genome (mitogenome) of this family also remain limited. In the present study, we describe the complete mitogenome of Camarochiloides weiweii, the first mitogenome sequenced for this family. This mitogenome consists of 13 protein-coding genes, two rRNA genes and 21 tRNA genes. Two tRNA gene rearrangements in this genome, including the translocation of trnA and trnR as well as the transposition of trnH, were observed and could be explained by the tandem duplication-random loss (TDRL) model. Bayesian and maximum likelihood analyses based on sequences of three different mitogenomic datasets recovered the monophyly of Reduvioidea, and the sister relationship between Reduvioidea and the remaining Cimicomorpha lineages. This study enlightens the future application of mitogenomic data in the phylogenetic study of Cimicomorpha based on the large-scale sampling.

Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura

Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Here we determined the complete mitogenome sequence of Chiromantes eulimene (Brachyura: Sesarmidae) for the first time. The total length is 15,894 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, as well as a putative control region. The genome composition is highly A + T biased (75.5%), and exhibits a negative AT-skew (−0.017) and GC-skew (−0.206). All of the 13 PCGs are initiated by the start codon ATN, with an exception (GTG) in ND1. The typical stop codon (TAA or TAG) is detected in ten PCGs, whereas the remaining three PCGs (COI, COII and Cyt b) terminate by an incomplete T. The gene order in C. eulimene mitogenome was rearranged compared with that of the ancestor of Decapoda. The gene order of F-ND5-H changed to H-F-ND5. Like other sesarmid crabs, the I-Q-M gene cluster in the pancrustacean ground pattern became Q-I-M order in C. eulimene genome. Tandem duplication-random loss model and slipped-strand mispairing mechanism are determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis places all Sesarmidae species into one group. Almost all families except Xanthidae, Gecarcinidae and Homolidae form a monophyletic clade and the polyphyly of Eriphioidea, Ocypodoidea and Grapsoidea is well supported. These results will help to better understand the gene rearrangements and evolutionary position of C. eulimene and lay a foundation for further phylogenetic studies of Brachyura.

Characterization of the complete mitochondrial genome of Amblyomma ovale, comparative analyses and phylogenetic considerations.

In this study, we sequenced two complete mitochondrial genomes of Amblyomma ovale, a tick of public health importance. Sequencing two distinct individuals, the resulting mitochondrial genomes were 14,756 and 14,760 bp in length and maintained the same gene order previously reported in Amblyomma. These were combined with RNA-seq derived mitochondrial sequences from three additional species, Amblyomma aureolatum, Amblyomma maculatum, and Amblyomma moreliae, to carry out mitogenome comparative and evolutionary analyses against all previously published tick mitochondrial genomes. We described a derivative genome rearrangement that isolates Ixodes from the remaining Ixodidae and consists of both a reverse translocation as well as an event of Tandem Duplication Random Loss. Genetic distance analyses indicated that cox2, nd1, nd5, and 16S are good candidates for future population studies in A. ovale. The phylogenetic analyses corroborated the utility of complete mitochondrial genomes as phylogenetic markers within the group. This study further supplements the genome information available for Amblyomma and facilitates future evolutionary and population genetic studies within the genus.

The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora.

Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.

The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae)

We present here a combined mitogenome gene order dataset totalling 62% of the known genera of East Asian potamiscine freshwater crabs that includes first-time mitogenome data for 14 species and gene order data from 37 other species of potamiscines. A surprisingly high number of mitogenome gene order rearrangements were found in the taxa studied (comprising nine different rearrangements and seven major patterns, one of which has two sub-arrangements). Our phylogenetic reconstructions indicate that the mitogenome gene order rearrangements are associated with the evolutionary history of potamiscine lineages. We also used a new Event-based Maximum Parsimony method to reconstruct ancestral gene orders, which takes into consideration gene duplication, pseudogeneticization, and tandem duplication random loss. Furthermore, shared mitogenome gene order patterns were used to inform the taxonomic placement of Sinopotamon parvum, and the cryptic diversity in Potamiscus. The remarkably frequent mitogenome rearrangements in potamiscine freshwater crabs have great potential to contribute to our understanding of the evolutionary history of these highly diverse decapods in East Asia.

The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M.verrilli: Novel gene arrangements and phylogenetic implications.

Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication–random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.

Deep transcriptome profiling sheds light on key players in nucleus implantation induced immune response in the pearl oyster Pinctada martensii

Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Here we determined the complete mitogenome sequence of Chiromantes eulimene (Brachyura: Sesarmidae) for the first time. The total length is 15,894 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, as well as a putative control region. The genome composition is highly A + T biased (75.5%), and exhibits a negative AT-skew (−0.017) and GC-skew (−0.206). All of the 13 PCGs are initiated by the start codon ATN, with an exception (GTG) in ND1. The typical stop codon (TAA or TAG) is detected in ten PCGs, whereas the remaining three PCGs (COI, COII and Cyt b) terminate by an incomplete T. The gene order in C. eulimene mitogenome was rearranged compared with that of the ancestor of Decapoda. The gene order of F-ND5-H changed to H-F-ND5. Like other sesarmid crabs, the I-Q-M gene cluster in the pancrustacean ground pattern became Q-I-M order in C. eulimene genome. Tandem duplication-random loss model and slipped-strand mispairing mechanism are determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis places all Sesarmidae species into one group. Almost all families except Xanthidae, Gecarcinidae and Homolidae form a monophyletic clade and the polyphyly of Eriphioidea, Ocypodoidea and Grapsoidea is well supported. These results will help to better understand the gene rearrangements and evolutionary position of C. eulimene and lay a foundation for further phylogenetic studies of Brachyura.

Sorting Signed Permutations by Inverse Tandem Duplication Random Losses.

Gene order evolution of unichromosomal genomes, for example mitochondrial genomes, has been modelled mostly by four major types of genome rearrangements: inversions, transpositions, inverse transpositions, and tandem duplication random losses. Generalizing models that include all those rearrangements while admitting computational tractability are rare. In this paper, we study such a rearrangement model, namely the inverse tandem duplication random loss (iTDRL) model, where an iTDRL duplicates and inverts a continuous segment of a gene order followed by the random loss of one of the redundant copies of each gene. The iTDRL rearrangement has currently been proposed by several authors suggesting it to be a possible mechanisms of mitochondrial gene order evolution. We initiate the algorithmic study of this new model of genome rearrangement by proving that a shortest rearrangement scenario that transforms one given gene order into another given gene order can be obtained in quasilinear time. Furthermore, we show that the length of such a scenario, i.e., the minimum number of iTDRLs in the transformation, can be computed in linear time.

A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea)

Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. This is the first report on a mitogenome of the superfamily Arionoidea, and indeed on a terrestrial slug. The mitogenome of Meghimatium bilineatum comprises 13,972 bp and exhibits a novel, highly distinctive gene arrangement among the Stylommatophora. Phylogenetic reconstructions based on the sequences of all protein-coding genes consistently recovered Meghimatium bilineatum as sister-group of the Succineidae. A phylogenetic reconstruction based on gene order, however, suggested a highly divergent tree topology, which is less credible when taking into account prior knowledge of stylommatophoran relationships. Our CREx (Common interval Rearrangement Explorer) analysis suggested that three successive events of tandem duplication random loss (TDRL) best explain the evolutionary process of gene order rearrangement in Meghimatium bilineatum from an ancestral stylommatophoran mitogenome. The present example offers new insights into the mechanisms of mitogenome rearrangements in gastropods at large and into the usefulness of mitogenomic gene order as a phylogenetic marker.

Mitochondrial genome of Phalantus geniculatus (Hemiptera: Reduviidae): trnT duplication and phylogenetic implications.

Reduviidae is the second largest family of Heteroptera and most of them are important natural enemies of agricultural and forest pests. Most of the sequenced mitochondrial (mt) genomes in this family have the typical gene arrangement of insects and encode 37 coding genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes). In the present study, we sequenced the mt genome of Phalantus geniculatus from the subfamily Peiratinae through high-throughput sequencing and encountered the duplication of tRNA genes for the first time in this subfamily. We identified 23 tRNA genes, including 22 tRNAs commonly found in insect mt genomes and an extra trnT (trnT2), which has high sequence similarity (96.9%) to trnT1. The presence of a "pseudo-trnP" in the non-coding region between trnT1 and trnT2 supports the hypothesis that the presence of an extra trnT can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic results inferred from mt genome sequences supported a sister relationship between Phymatinae and the remaining sampled subfamilies, as well as a paraphyletic Reduviinae. The present study highlights the utility of mt genomes in the phylogenetic study of Reduviidae based on the large scale taxon sampling in the future.

EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements

BackgroundTo study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it.ResultsWe present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes.ConclusionEqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes. EqualTDRL is implemented in C++ using the ggplot2 package of the open source programming language R and is freely available from http://pacosy.informatik.uni-leipzig.de/equaltdrl.

An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements.

The preserving Genome Sorting Problem (pGSP) asks for a shortest sequence of rearrangement operations that transforms a given gene order into another given gene order by using rearrangement operations that preserve common intervals, i.e., groups of genes that form an interval in both given gene orders. The wpGSP is the weighted version of the problem were each type of rearrangement operation has a weight and a minimum weight sequence of rearrangement operations is sought. An exact algorithm - called CREx2 - is presented, which solves the wpGSP for arbitrary gene orders and the following types of rearrangement operations: inversions, transpositions, inverse transpositions, and tandem duplication random loss operations. CREx2 has a (worst case) exponential runtime, but a linear runtime for problem instances where the common intervals are organized in a linear structure. The efficiency of CREx2 and its usefulness for phylogenetic analysis is shown empirically for gene orders of fungal mitochondrial genomes.

A transfer RNA gene rearrangement in the lepidopteran mitochondrial genome

Gene arrangements in the mitochondrial genomes (mitogenomes) of insects are conserved across the major lineages, but can be rearranged within derived groups and may provide valuable phylogenetic characters. In this study, we sequenced the entire mitogenome of Parasa consocia, a moth of the family Limacodidae (Lepidoptera: Zygaenoidea). Compared with other lepidopterans and ancestral insects, the P. consocia mitogenome features a transfer RNA gene arrangement novel among lepidopterans between the ND3 and ND5 genes: RANSEF (the underline signifies an inverted gene), which differs from the ARNSEF arrangement of ancestral insects. This rearrangement can be explained by the tandem duplication-random loss model. We inferred a phylogenetic hypothesis for the lepidopteran superfamily based on mitochondrial amino-acid sequences using the Bayesian-inference and maximum-likelihood methods. Our results showed that P. consocia belongs to the Zygaenoidea superfamily and supported the following phylogenetic relationship: Yponomeutoidea + (Tortricoidea + Zygaenoidea + (Papilionoidea + (Pyraloidea + (Noctuoidea + (Geometroidea + Bombycoidea)))))). Comparative analyses indicated that mitogenomes are a useful phylogenetic tool at the subfamily level within the order Lepidoptera. Our findings also suggest that mitogenomes are likely to represent a valuable tool for systematics in other groups of lepidopterans.

Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes

The tandem duplication random loss operation (TDRL) is an important genome rearrangement operation in metazoan mitochondrial genomes. A TDRL consists of a duplication of a contiguous set of genes in tandem followed by a random loss of one copy of each duplicated gene. This paper presents an analysis of the combinatorics of TDRLs on circular genomes, e.g., the mitochondrial genome. In particular, results on TDRLs for circular genomes and their linear representatives are established. Moreover, the distance between gene orders with respect to linear TDRLs and circular TDRLs is studied. An analysis of the available animal mitochondrial gene orders shows the practical relevance of the theoretical results.

Duplication and Remolding of tRNA Genes in the Mitochondrial Genome of Reduvius tenebrosus (Hemiptera: Reduviidae).

Most assassin bugs are predators that act as important natural enemies of insect pests. Mitochondrial (mt) genomes of these insects are double-strand circular DNAs that encode 37 genes. In the present study, we explore the duplication and rearrangement of tRNA genes in the mt genome of Reduvius tenebrosus, the first mt genome from the subfamily Reduviinae. The gene order rearranges from CR (control region)-trnI-trnQ-trnM-ND2 to CR-trnQ-trnI2-trnI1-trnM-ND2. We identified 23 tRNA genes, including 22 tRNAs commonly found in insects and an additional trnI (trnI2), which has high sequence similarity to trnM. We found several pseudo genes, such as pseudo-trnI, pseudo-CR, and pseudo-ND2, in the hotspot region of gene rearrangement (between the control region and ND2). These features provided evidence that this novel gene order could be explained by the tandem duplication/random loss (TDRL) model. The tRNA duplication/anticodon mutation mechanism further explains the presence of trnI2, which is remolded from a duplicated trnM in the TDRL process (through an anticodon mutation of CAT to GAT). Our study also raises new questions as to whether the two events proceed simultaneously and if the remolded tRNA gene is fully functional. Significantly, the duplicated tRNA gene in the mitochondrial genome has evolved independently at least two times within assassin bugs.

Complete mitochondrial genomes of two gelechioids, Mesophleps albilinella and Dichomeris ustalella (Lepidoptera: Gelechiidae), with a description of gene rearrangement in Lepidoptera

We sequenced the entire mitochondrial genome (mitogenome) of two gelechioids, Mesophleps albilinella and Dichomeris ustalella, and compared their genome organization and sequence composition to those of available gelechioid mitogenomes for an enhanced understanding of Gelechioidea genomic characteristics. We compared all available lepidopteran mitogenome arrangements, including that of M. albilinella, which is unique in Gelechioidea, to comprehend the extensiveness and mechanisms of gene rearrangement in Lepidoptera. The genomes of M. albilinella and D. ustalella are 15,274 and 15,410bp in size, respectively, with the typical sets of mitochondrial (mt) genes. The COI gene begins with CGA (arginine) in all sequenced gelechioids, including M. albilinella and D. ustalella, reinforcing the feature as a synapomorphic trait, at least in the Gelechioidea. Each 353- and 321-bp long A+T-rich region of M. albilinella and D. ustalella contains one (D. ustalella) or two (M. albilinella) tRNA-like structures. The M. albilinella mitogenome has a unique gene arrangement among the Gelechioidea: ARNESF (the underline signifies an inverted gene) at the ND3 and ND5 junction, as opposed to the ARNSEF that is found in ancestral insects. An extensive search of available lepidopteran mitogenomes, including that of M. albilinella, turned up six rearrangements that differ from those of ancestral insects. Most of the rearrangements can be explained by the tandem duplication-random loss model, but inversion, which requires recombination, is also found in two cases, including M. albilinella. Excluding the MIQ rearrangement at the A+T-rich region and ND2 junction, which is found in nearly all Ditrysia, most of the remaining rearrangements found in Lepidoptera appear to be independently derived in that they are automorphic at several taxonomic scales, although current mitogenomic data are limited, particularly for congeneric data.

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

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.