Mitogenomic Characteristics Research Articles

Low-coverage genome sequencing yields the complete mitogenome of Pyjama Slug, Chromodoris quadricolor (Mollusca: Chromodorididae)

In this study, the complete mitogenome sequence of Pyjama Slug, Chromodoris quadricolor (Mollusca: Chromodorididae), has been decoded for the first time by low-coverage genome-sequencing method. The overall base composition of C. quadricolor mitogenome is 30.6% for A, 14.4% for C, 17.8% for G and 37.2% for T and has low GC content of 32.2%. The assembled mitogenome, consisting of 14 259 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs genes. The C. quadricolor mitogenome has the common mitogenome gene organization and feature of Nudipleura (a clade of sea slugs and sea snails). The complete mitogenome provides essential and important DNA molecular data for further evolutionary analysis for sea slugs and sea snails.

The complete mitogenome of the Galaxy Coral, Galaxea fascicularis (Cnidaria: Oculinidae)

In this study, the complete mitogenome sequence of Galaxy Coral, Galaxea fascicularis (Cnidaria: Oculinidae), has been sequenced by next-generation sequencing method. The overall base composition of Galaxea fascicularis mitogenome is 24.9% for A, 14.0% for C, 24.3% for G and 36.8% for T and has low GC content of 38.3%. The assembled mitogenome, consisting of 18 751 bp, has unique 13 protein-coding genes (PCGs), three transfer RNAs and two ribosomal RNAs genes. The G. fascicularis mitogenome has the common mitogenome gene organization and feature of scleractinian coral. Among 13 PCGs, ND5 gene is interrupted by group I intron (12 022 bp). There are 12 genes embedded in ND5 group I intron (tRNA-Leu, ND1, CYTB, ND2, ND6, ATP6, ND4, 12S rRNA, COX3, COX2, ND4L and ND3). The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral.

Complete mitochondrial genome of the spotted-wing drosophila, Drosophila suzukii (Diptera: Drosophilidae)

The spotted-wing drosophila, Drosophila suzukii (Diptera: Drosophilidae) is an Asian species introduced into North America and Europe. It damages a wide variety of thin-skinned fruits. We sequenced the complete mitochondrial genome (mitogenome) to better understand the mitogenomic characteristics of this species. The 16 230-bp complete mitogenome of the species consists of a typical set of genes, including 13 protein-coding genes (PCGs), two rRNA genes and 22 tRNA genes, and one major non-coding A + T-rich region, with an arrangement typical of insects. Twelve PCGs began with the typical ATN codon, whereas the COI began with TCG, which has been designated as the start codon for other Drosophila species. The 1525-bp A + T-rich region is the second longest in Drosophila species for which the whole mitogenome has been sequenced, after D. melanogaster. Phylogenetic analysis using the 13 PCGs of the Drosophila species indicated that D. suzukii is placed, with a strong support, in the basal lineage of the previously defined Melanogaster group.

Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations.

To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.

The complete mitochondrial genome of Cosmoscarata bispecularis (Hemiptera, Cicadomorpha, Cercopoidea, Cercopidae)

To characterize froghopper mitochondrial genome (mitogenome) features, in this study, the mitochondrial genome of Cosmoscarata bispecularis (Hemiptera, Cicadomorpha, Cercopoidea, Cercopidae) was sequenced and annotated. The complete genome is 15,426 bp in length. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (A + T-rich region). All the PCGs initiate with the standard start codons ATN and all the tRNAs can be folded into typical cloverleaf secondary structures except tRNASer(GCT), which only formed a simple loop. The control region is consisted of 861 bp bases located between the srRNA gene and the tRNAlle–tRNAGln–tRNAMet(IQM) gene cluster. The measure of complete mitogenome sequence of C. bispecularis will provide fundamental data for the phylogenetic and biogeographic studies of the Cercopoidea and Hemiptera.

The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera.

BackgroundZoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera.ResultsThe mitogenome of Zorotypus medoensis with an A + T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A + T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees.ConclusionsCharacterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1156) contains supplementary material, which is available to authorized users.

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A+T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNAGln and ND2 (64–87bp), conserved ATACTAA motif between tRNASer (UCN) and ND1, and characteristic features of the A+T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNAAsn/tRNASer (AGN), instead of the rearrangement tRNASer (AGN)/tRNAAsn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea+Noctuoidea+Geometroidea)+Pyraloidea)+Papilionoidea)+Tortricoidea)+Yponomeutoidea)+Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae+(Hesperiidae+(Pieridae+((Lycaenidae+Riodinidae)+Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.

Extreme sequence divergence between mitochondrial genomes of two subspecies of White-breasted Wood-wren (Henicorhina leucosticta, Cabanis, 1847) from western and central Panamá

Prior studies of mitochondrial variation in White-breasted Wood-Wrens (Henicorhina leucosticta) have suggested that populations in South American and Mesoamerica might represent multiple species. Here we report the complete mitochondrial genomes from two individuals of H. leucosticta, representing the Panamanian subspecies pittieri and alexandri. The two sequences were 16,721 and 16,726 base pairs in size with both genomes comprised of the usual 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and one displacement loop region in the standard avian order. Uncorrected pairwise divergence between mitogenome features was high, with the highest divergence occurring in protein-coding genes (average = 8.2%), followed by control region (6.7%). RNA features had lower pairwise divergences (average tRNA = 4.3%, average rRNA = 2.3%). The protein-coding ATPase 6 gene had a different stop codon between these two specimens. The high level of sequence variation between these subspecies suggests that Mesoamerican H. leucosticta might be comprised of multiple species. We urge a full phylogeographic survey of this widespread Neotropical forest bird.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).

BackgroundComparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012).ResultsWe present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure.ConclusionsNext-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.

鳞翅目昆虫比较线粒体基因组学研究进展

Lepidopteran insects have a marked impact on human society, whether functioning as major pests of agriculture and forestry, pollinators, or a primary producer of silk. Insect mitochondrial genome (mitogenome) has a relatively conserved gene content and gene order, so it has been widely used in molecular phylogeny and evolution. To date, complete mitogenomes have been sequenced for a total of 63 species of Lepidoptera. Among the sequenced mitogenomes, however, only 58 are reference sequences available in GenBank. Here, a comparative analysis of all the mitogenome reference sequences revealed some basic features of lepidopteran mitogenomes. Furthermore, the phylogenetic relationships within Lepidoptera based on the complete mitogenome sequences proved to be similar to that based on traditional morphological characters. This work paves the way for better understanding of the evolution of lepidopteran insects, and suggests that comparative mitogenomic analysis has great potential for resolving phylogenetic relationships among the major groups of insects at the dawn of the postgenomic era.

Complete mitochondrial genome of the endangered Asian giant softshell turtle Pelochelys cantorii (Testudinata: Trionychidae)

The complete mitogenomes of the endangered Asian giant softshell turtle Pelochelys cantorii (Testudinata: Trionychidae) were first determined from two living specimens, with the lengths of 17,612 and 17,499 bp, which showed the typical mitogenomic characteristics of vertebrates. An A+1 frameshift mutation at position 174 of the ND3 gene was identified. Seven point mutations were found between the two mitogenomes. The length variation of the two mitogenomes was due to the different repeat numbers of the tandem motifs in the control regions.

Determination and comparison of two complete mitochondrial genomes of golden Chinese loach, Sinibotia superciliaris (Teleostei, Cypriniformes)

The golden Chinese loach, Sinibotia superciliaris (Günther, 1892) is an endemic fish in China, which is only distributed in the main river and tributaries of the upper and middle Yangtze River. In this study, we sequenced two mitochondrial genomes simultaneously from two samples of S. superciliaris collected from two different locations. Both mitogenomes were 16,572 bp in length, showing a typical vertebrate mitogenome feature with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 major non-coding control region (CR). Alignment and comparative analyses showed that the two mitogenome sequences possessed 22 mutation sites, all of which were transitions and mainly occurred in protein-coding genes (13/22) and CR (7/22). Among the 13 mutation sites that occurred in protein-coding genes, three mutation sites occurred in the first codon position and the remaining 10 sites occurred in the third codon position. However, only one mutation that occurred in the first codon position resulted in non-synonymous substitution in COI gene. The molecular data presented in this study will contribute to further phylogenetic analyses for this group of fishes.

Comparative studies of the complete mitochondrial genomes of four Paphia clams and reconsideration of subgenus Neotapes (Bivalvia: Veneridae)

The extreme variability of the mitochondrial (mito) genomes of bivalves makes it difficult to understand their evolutionary dynamics, given that species from different families do not share comparable features. We compared the mitogenomes from four Paphia clams (three of them were firstly sequenced) and found that mitogenome reorganization among the four congeneric species is not random but follows phylogenetic trends. Start/stop codon variations are species-correlated rather than gene-correlated, and bear useful phylogenetic information. Unique start/stop codon usage in P. euglypta and A+T content in P. amabilis indicates that these mitogenome-level characters, usually considered to be conservative features in other lineages, may not be phylogenetically evolved, but may have evolved via species-specific mitogenomic maintenance mechanisms. Variable divergence of two trnM genes in different lineages may demonstrate differences in mechanisms by which paralogous trnM genes are maintained. Sequence alignment analysis indicates that the VNTRs in the four mitogenomes have a common origin. The rationale of the subgenus Neotapes Kuroda and Habe, 1971 was supported by evidence from morphological characters, mitogenomic features, as well as phylogenetic analyses using cox1 and rrnS genes. The data suggest that the taxonomic basis of the subgenus should be “smooth surface” but not “undulated lines,” and P. textile should be classified to the Neotapes subgenus.

Phylogenetic relationships among three new Hemibarbus mitogenome sequences belonging to the subfamily Gobioninae (Teleostei, Cypriniformes, and Cyprinidae)

Background and aims: Here, we present the full-length mitogenome sequences of Hemibarbus labeo, Hemibarbus longirostris, and Hemibarbus mylodon – three fish species belonging to the subfamily Gobioninae (Teleostei, Cypriniformes, and Cyprinidae). H. mylodon is endemic to the Korean Peninsula and a critically endangered freshwater species because of various anthropogenic activities around its natural habitat.Results: Overall characteristics of mitogenomes of the three Hemibarbus species were identical to previously known typical vertebrate mitogenomes. Bayesian inference of phylogeny recovered the monophyly of the subfamily Gobioninae with high posterior probability support, with the three Hemibarbus species forming a strongly supported monophyletic group. H. mylodon was placed at the basal position, and H. longirostris was separated from two monophyletic H. labeo types.Conclusion: Our findings are congruent with the previous taxonomic appraisal based on morphological analysis.

Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features

We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.