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The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp ( Cyclidia fractifasciata ) to 15,749 bp ( Ophthalmitis albosignaria ) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM . Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.

The complete mitochondrial genome of Episymploce splendens, 15,802 bp in length, was determined and annotated in this study. The mito-genome included 13 PCGs, 20 tRNAs and 2 rRNAs. Unlike most typical mito-genomes with conservative gene arrangement and exceptional economic organization, E. splendens mito-genome has two tRNAs (tRNA-Gln and tRNA-Met) absence and a long intergenic spacer sequence (93 bp) between tRNA-Val and srRNA, showing the diversified features of insect mito-genomes. This is the first report of the tRNAs deletion in blattarian mito-genomes and we supported the duplication/random loss model as the origin mechanism of the long intergenic spacer. Two Numts, Numt-1 (557 bp) and Numt-2 (975 bp) transferred to the nucleus at about 14.15 Ma to 22.34 Ma, and 19.19 Ma to 24.06 Ma respectively, were found in E. splendens. They can be used as molecular fossils in insect phylogenetic relationship inference. Our study provided useful data for further studies on the evolution of insect mito-genome., Competing Interests: The authors have declared that no competing interests exist.

Background: Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae., Results: We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny., Conclusions: This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA). Three different types of short tandem repeats in the N. rhombifolia control region (CR) were observed. The homologous alignments of these tandem repeats with other six cockroach mitogenome CRs revealed a low similarity. Three conserved sequence blocks (CSB) were detected in both cockroach mitochondrial CRs. CSB1 was specific for blattinine mitogenomes and was highly conserved with 95% similarity, speculating that this block was a possible molecular synapomorphy for this subfamily. CSB3 located nearby downstream of CSB1 and has more variations within blattinine mitogenomes compared with CSB1. The CSB3 was capable of forming stable stem-loop structure with a small T-stretch in the loop portion. We assessed the influence of four datasets and two inference methods on topology within Orthopteroidea. All genes excluding the third codon positions of PCGs could generate more stable topology, and higher posterior probabilities than bootstrap values were presented at some branch nodes. The phylogenetic analysis with different datasets and analytical methods supported the monophyly of Dictyoptera and supported strongly the proposal that Isoptera should be classified as a family (Termitidae) of the Blattaria. Specifically, Shelfordella lateralis was inserted in the clade Periplaneta. Considering the K2P genetic distance, morphological characters, and the phylogenetic trees, we suggested that S. lateralis should be placed in the genus Periplaneta.

The evolutionary history of macaques, genus Macaca, has been under debate due to the short times of divergence. In this study, maternal, paternal, and biparental genetic systems were applied to infer phylogenetic relationships among macaques and to trace ancient hybridization events in their evolutionary history. Using a PCR display method, 17 newly phylogenetically informative Alu insertions were identified from M. assamensis. We combined presence/absence analysis of 84 Alu elements with mitochondrial genomes as well as nuclear sequences (five autosomal genes, two Y chromosomal genes, and one X chromosomal fragment) to reconstruct a robust macaque phylogeny. Topologies generated from different inherited markers were similar supporting six well defined species groups and a close relationship of M. assamensis and M. thibetana, but differed in the placing of M. arctoides. Both Alu elements and nuclear genes supported that M. arctoides was close to the sinica group, whereas the mitochondrial data clustered it into the fascicularis/mulatta lineage. Our results reveal that a sex-biased hybridization most likely occurred in the evolutionary history of M. arctoides, and suggest an introgressive pattern of male-mediated gene flow from the ancestors of M. arctoides to the M. mulatta population followed by nuclear swamping. According to the estimation of divergence dates, the hybridization occurred around 0.88~1.77 mya (nuclear data) or 1.38~2.56 mya (mitochondrial data). In general, our study indicates that a combination of various molecular markers could help explain complicated evolutionary relationships. Our results have provided new insights into the evolutionary history of macaques and emphasize that hybridization might play an important role in macaque evolution.

The complete mitochondrial genome of L. edwardsi was first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand protein-coding genes of L. edwardsi and other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated that L. edwardsi was closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward's long-tailed rat is more suitable to be classified into genus Leopoldamys and named as Leopoldamys edwardsi. This study suggested that R. edwardsi is inappropriate for the other name of L. edwardsi.

The blister beetle is an important resource insect due to its defensive substance cantharidin, which was widely used in pharmacology and plant protection. We determined the complete mitochondrial genome of Epicauta chinensis Laporte (Coleoptera: Tenebrionoidae: Meloidae). The circular genome is 15,717 bp long, encoding 13 protein-coding genes (PCGs), two ribosomal RNAs and 22 tRNAs and containing a A+T-rich region with gene arrangement identical to other Coleopteran species. Twelve PCGs start with typical ATN codon, while ATP8 gene initiate with GTT for first report in Insecta. All PCGs terminate with conventional stop codon TAA or TAG. All tRNAs in E. chinensis are predicted to fold into typical cloverleaf secondary structure, except tRNA-Ser(AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem-loop structure. The secondary structure of lrRNA and srRNA comprises 48 helices and 32 helices respectively. The 1101 bp A+T-rich region contains a 15 bp poly-T stretch and microsatellite-like repeats rather than large tandem repetitive sequences. Phylogenetic analysis, based on 13 PCGs of 45 Coleopteran species, show that E. chinensis grouped with Tenebrionidae species. It also support the topology of (((Chrysomelidae+Curculionoidea)+(Cucujoidea+Cleroidea))+Tenebrionoidea) within Cucujiformia., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Vibrissaphora boringii (Anura: Megophryidae) is an endemic precious species of China. In this paper, we determined the complete nucleotide sequence of the mitochondrial genome of the V. boringii. The entire mtDNA sequence was 17,085 bp in length, which contained 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and 1 displacement loop (D-loop). The base composition was 27.7% A, 25.5% C, 15.4% G and 31.5% T, with a much higher A + T content. Except for eight tRNAs and nd6 genes, all other mitochondrial genes were encoded on the heavy strand (H-strand). Molecular data presented here provide a useful tool for resolving phylogenetic and genetic problems related to this species.

The Cricetulus kamensis is endemic to China and is popular as pet. In the present study, the complete mitogenome of C. kamensis was first determined. It was 16,270 bp in length and the composition and arrangement of its genes are analogous to most other mammals. The overall base composition of heavy strand is 33.2% A, 26.8% T, 27.2% C and 12.7% G. The sequence is highly G-C poor (∼40%) and A is the most numerous nucleotide followed by T >C >G, which is similar to other mammalian mitochondrial genomes. It is notable that three extra bases "CAT" were inserted in cytb at the 3' end position and no stop codon was found for this coding region. The mitogenome sequence of C. kamensis could contribute to a better solution of its phylogenetic position and phylogenetic relationship within Cricetinae in the future.

The Pearl-banded rat-snake Elaphe perlacea (recently renamed Euprepiophis perlacea) belongs to the family Colubridae, and is only distributed in western Sichuan Province, China. In this study, the whole mitochondrial genome of E. perlacea was first sequenced. It was determined to be 17,160 bp and included 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions (D-loop). Except for eight tRNAs and nd6 genes, all other mitochondrial genes were encoded on the heavy strand (H strand). Molecular data presented here provide a useful tool for helping set the stage for further studies and the molecular evolution of the mitochondrial genome.

The complete mitochondrial genome of Assamese macaques (Macaca assamensis) was sequenced in this study. The genome is 16,542 bp long, consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding areas. Eight PCGs (COI, COII, ATP6, COIII, ND4L, ND4, ND6, CYTB) initiate with the start codon ATG and another two genes (ND1, ATP8) use GTG, while ND2, ND3 and ND5 start with ATT, ATC and ATA, respectively. Five genes (COII, ATP8, ATP6, ND4L and ND5) use the complete stop codon TAA, whereas four genes have incomplete stop codons, TA- (COIII) and T- - (ND3, ND4, CYTB), while others use standard canonical TAA as their termination codons. The largest non-coding control region with the length of 1091 bp is located between the tRNA-Pro and tRNA-Phe genes.

The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents' mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.

The Black Stork, Ciconia nigra belongs to family Ciconiidae, which is evaluated as Least Concern by IUCN. In this study, the complete mitochondrial genome of C. nigra was first sequenced and characterized, which was 17,795 bp in length. The mt-genome has tandem repeats of 80 bp and 78 bp repeat units, and AAACAAC and AAACAAACAAC tandem repeats in D-loop region. It is notable that a single extra base "C" at position 174 was inserted in gene ND3. Bayesian inference, maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand protein-coding genes. Phylogenetic analyses showed that Ardeidae diverged earlier than Ciconiidae, Cathartida and Threskiornithidae, and Ciconiidae had closest relationship to Cathartida. C. nigra diverged first among three Ciconia birds.

The Hainan partridge, Arborophila ardens belongs to family Phasianidae, and distributes only in Hainan, China. In this study, the complete mitochondrial genome of A. ardens was first sequenced and characterized. The genome is 16,727 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes located on the heavy strand. Phylogenetic analyses further confirm the Arborophila placed at the root of Phasianidae. Arborophila ardens show closer relationship with A. rufipectus than A. rufogularis and A. gingica which cluster as sister group to A. ardens and A. rufipectus.

The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.

The mountain weasel (Mustela altaica) belongs to family Mustelidae, which is the near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of M. altaica was sequenced and characterized. The genome is 16,521 bases in length (GenBank accession no. KC815122). The nucleotide sequence data of 12 heavy-strand protein-coding genes of M. altaica and other 20 Mustelidae species were used for phylogenetic analyses. Trees constructed by using Bayesian inference, maximum parsimony and maximum likelihood demonstrated that M. altaica was close to Mustela nivalis and they were sister to Mustela putorius and Mustela sibirica.

Tetraophasis szechenyii and T. obscurus are endangered phasianid birds endemic to China. Historically, the question of whether T. obscurus and T. szechenyii are valid species or subspecies has been controversial. In order to clarify their phylogenetic relationship, we sequenced the complete mitochondrial genome of T. obscurus and, using the complete mitochondrial genome of T. szechenyii, which our lab had already sequenced, conducted Bayesian and maximum-likelihood phylogenetic analyses based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. Genetic distance and divergence time between the two species were also calculated. The complete mitochondrial genome of T. obscurus was 16,707 bases (accession no.: NC_018034), and its structure was similar to mitochondrial genomes reported for other phasianids. The genetic distance between T. obscurus and T. szechenyii was 0.028, and the divergence time of T. obscurus and T. szechenyii was 1.75 Myr. Considering the genetic distance and divergence time, as well as geographical distribution and morphological differences, we suggest that T. obscurus and T. szechenyii are two valid species. The Pleistocene glacial events in the Hengduan Mountains region may have played an important role in the speciation of T. obscurus and T. szechenyii.

The rice leafroller, Cnaphalocrocis medinalis, is one of the most important pests on rice and possesses striking flight ability. We have determined the nucleotide sequence of the 15,377 bp of a C. medinalis mitochondrial genome (mtDNA). The mtDNA encodes 37 genes and shows a unique lepidopteran CR-M-I-Q arrangement. Three possible substructures were detected in C. medinalis and some other lepidopteran insects' control region. The findings might be relevant to the regulation of mtDNA replication and transcription. Phylogenetic relationships were reconstructed among 19 families in Lepidoptera so far. Cnaphalocrocis medinalis forms a reciprocal monophyletic group with Ostrinia in clade Crambidae instead of Pyralidae. The topology between Papilionoidea and other superfamilies showed an apparent contradiction with traditional Lepidopteran classification. As a well-known migratory insect, the molecular information contained in C. medinalis mtDNA may provide a further insight into the evolution of mitochondria genes and insect species, and may help to better understanding the energy metabolism of invertebrates.

Though extensive efforts have been made to investigate the phylogeny of the Cetartiodactyla, the relationships within the Cetartiodactyla, especially the position of the family Moschidae among Ruminantia families, still remain controversial. To further clarify these relationships, we sequenced the mitochondrial genome of the Alpine musk deer (Moschus chrysogaster), which is an endemic endangered species from China. Then, we conducted molecular phylogenetic analyses of the Alpine musk deer and 49 other species on the basis of Bayesian and maximum likelihood methods. The results show that the Moschidae is the sister group of the Bovidae, both of which form a clade that clusters with the Cervidae. The cetaceans are nested within the Artiodactyla as the sister group of the Hippopotamidae. Among the musk deer, M. chrysogaster and M. berezovskii are more closely related to each other than to M. moschiferus.

The blood pheasant Ithaginis cruentus belongs to the family Phasianidae and distributes in the eastern Himalayas, India, Nepal, Bhutan and China. In this study, the total mitochondrial genome of I. cruentus was firstly determined. The genome is 16,683 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirmed that Ithaginis clearly diverged later than Arborophila, and Arborophila was a basal branch within Phasianidae.

The total length of the Bufo tibetanus mitochondrial genome sequence is 17,405 bp. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 displacement loop (D-loop). Except for eight tRNAs and nd6 genes, all other mitochondrial genes are encoded on the heavy strand (H strand). Most of the 22 tRNA genes can fold into a typical cloverleaf secondary structure by tRNAscan-SE, except for tRNA(Ser). Molecular data presented here provide a useful toll for helping set the stage for further studies and the molecular evolution of the mitochondrial genome.

The Shrew Gymnure Neotetracus sinensis belongs to family Erinaceidae, and distributes in China, Myanmar, and northern Vietnam. In this study, the whole mitochondrial genome of N. sinensis was first sequenced and characterized. The genome is 16,982 bases in length. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirm the subfamily Galericinae diverged prior to the subfamily Erinaceinae, support the species N. sinensis was in distinct genus Neotetracus rather than Hylomys, and N. sinensis diverged later than Echinosorex gymnura.

The first complete mitochondrial genome of the large white-bellied rat (Niviventer excelsior) was sequenced and annotated in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The mitochondrial genome sequence (16,298 bp) of N. excelsior contains 13 protein-coding, 2 rRNA and 22 tRNA genes as well as 1 typical control region (D-Loop), which are shared by other mammalian mitochondrial genomes. The codon usage also followed the typical vertebrate pattern except for an unusual CCA stop codon, which was termination codon of Cyt b. The 16 nucleotide insertion was detected in the central conserved domain of d-Loop. The 12 heavy-strand encoded protein-coding genes were used to reconstruct the phylogenetic relationships by the Bayesian inference and maximum likelihood methods. Topologies revealed that N. excelsior clustered together with the species in genus Rattus, indicating their closer phylogenetic relationship.

The Gracile shrew mole (Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys.

The Chinese oriental vole (Eothenomys chinensis) belongs to subfamily Arvicolinae, which is endemic to the mountains in southwest China. E. chinensis and other Arvicoline species display a number of features that make them ideal for evolutionary studies of speciation and the role of Quaternary glacial cycles on diversification. In this study, the complete mitochondrial genome of E. chinensis was sequenced. It was determined to be 16,362 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of E. chinensis and other 19 rodents were used for phylogenetic analyses. Trees constructed using three different phylogenetic methods (Bayesian, maximum parsimony, and maximum likelihood) showed a similar topology demonstrating that E. chinensis was clustered in subfamily arvicolinae--formed a solid monophyletic group being sister to the subfamily Cricetinae. And the trees also suggested that E. chinensis is a sister to the genus Microtus and Proedromys.

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.

The Chinese scrub vole (Neodon irene) belongs to the subfamily Arvicolinae, which is restricted to mountain areas at high altitudes (2800-4000). In this study, we sequenced the complete mitochondrial genome of N. irene. It was determined to be 16,367 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. irene and other 22 rodents were used for phylogenetic analysis. Bayesian inference (BI) and maximum likelihood (ML) were used. Both the BI and ML trees demonstrated that Microtus rossiaemeridionalis and Microtus kikuchii did not cluster together with each other. On the contrary, M. rossiaemeridionalis showed close relationship with N. irene. In the present study, only one sequence from Neodon and two sequences from Microtus were included in the phylogenetic analysis which should contribute to the unusual relationship. Therefore, in order to better understand the phylogenetic relationship within Rodentia, more rodents' complete mitochondrial genomes are required.

AIM. The complete mitochondrial genome sequence of a newly discovered vole, Proedromys liangshanensis (Rodentia: Cricetidae: Arvicolinae), was determined. RESULTS. The mitogenome of P. liangshanensis is 16,296 bp in length. As with most other mammals, it contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. The A+T content of the control region is 58.2%, the lowest proportion detected so far in Myomorpha. To confirm the phylogenetic position of P. liangshanensis, we carried out phylogenetic analyses based on complete mitochondrial genomic data using Bayesian, maximum parsimony, and maximum likelihood methods. CONCLUSION. All results revealed that P. liangshanenis is sister to Microtus. Although the results do not bear light on the validity of the genus Proedromys, based on the morphological characters, we suggest that Proedromys is an independent genus of equal rank to the genus Microtus.

The sugarcane borer, Diatraea saccharalis (F.), is an economically important pest of several major crops in North and South America. There is great concern over potential resistance development to the valuable transgenic Bacillus thuringiensis corn. Cost-effective monitoring methods, especially regarding molecular markers that could detect early changes in resistance allele frequency in field populations of D. saccharalis, are needed. This article reports the complete mitochondrial genome sequence of D. saccharalis (GenBank: FJ240227). The mitochondrial genome sequence of D. saccharalis has the typical metazoan mitogenome structure including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, with a total size of 15,490 bp. The A+T content of the full mitogenome is 80.1% and the significant A+T bias is at the control region (94.9%), as compared to the extremely low G content (0.6%). In all 13 protein coding genes, 9 start with the common Met initiator codon (ATA or ATG) and 3 use ATT (Ile), whereas CGA (Arg) is used as a start codon in COI. Eleven of the 13 protein coding genes use complete termination codon (TAA), whereas COI and COII use incomplete ones, which terminated with a single T-nucleotide abutting on tRNA. There are seven major noncoding spacers (628 bp), including six intergenic spacers and an A+T-rich region, which are scattered in the mitogenome. Several microsatellite-like elements were observed in these noncoding regions. The complete mitochondrial sequences of D. saccharalis reported in this study can provide useful data in analyzing divergence of lepidopteran insects and in developing DNA-based diagnoses and genetic makers.

Rock carp, Procypris rabaudi (Tchang), is an endemic fish species in China. We sequenced the complete mitochondrial genome of it by high-fidelity polymerase chain reaction with conserved primers and primer walking sequencing method. The complete mitochondrial genome of rock carp is 16595 bp in length and contains 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of most other vertebrates. The origin of L-strand replication (OL) in rock carp mitochondrion is located in a cluster of five tRNA genes (WANCY region) with 35 nucleotides in length. The control region is located between the tRNA-Pro and tRNA-Phe genes and is 943 bp in length. Three conserved sequence blocks (CSB), an extended termination associated sequence (ETAS), an AT-repeat microsatellite sequence and a putative promoter sequence for H-strand transcription (HSP) were identified within this region. The microsatellite sequence has a very low variation, with only one repeat alteration in 50 checked individuals (from 12 to 13 repeats). The phylogenetic analysis for rock carp was performed with Bayesian and Maximum likelihood (ML) methods based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result suggested that traditional taxonomic barbines possibly originated more early than cyprininaes; rock carp was placed at the position between barbines and cyprininaes, while has a closer relationship with cyprininaes than barbines.

The complete sequence of the mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) has been determined by long and accurate polymerase chain reaction (LA-PCR) and with primer walking sequence method. The genome is 16728 bp in size, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes and one control region, demonstrating a structure very similar to that of other phasianids. In order to investigate the phylogenetic position of Arborophila within Phasianidae, the sequences of 12 concatenated heavy-strand encoded protein coding genes were used for phylogenetic analysis employing a Bayesian inference method, Maximum parsimony (MP) analyses and Maximum likelihood (ML) analysis. With the exception of a few nodes, most internal branches were supported by high Bayesian posterior probabilities (BPP) and bootstrap probabilities (BSP). Using the 12 mitochondrial protein-coding genes sequence, we performed the likelihood tests of competing tree topologies , and also tried to estimate the divergence time within Phasianidae by the global rate minimum deformation method (GRMD), both with the previously constructed ML tree using Treefinder (Jobb, G., 2008. TREEFINDER version of February 2007. Munich(Germany).) The combined strict consensus tree demonstrated that Arborophila rufipectus possessed a basal phylogenetic position within Phasianidae. Our results also showed that the turkey (Meleagris gallopavo) had a close relationship with the gallopheasant group, which may suggest that the turkey should be classified into the Phasianidae. In addition, Phasianus was found to share a closer relationship with Lophura than Syrmaticus with robust support.

The complete mitochondrial genome of Macaca thibetana was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequencing methods. It is 16,540 bp and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Most codon usage followed the typical pattern of vertebrates. Two rare start codons were found, in which GTG initiated the NADH dehydrogenase subunit 1 (ND1) gene and the ATP8 gene, and ATT initiated the ND2 gene. A new mitochondrial DNA-like sequence (2003 bp) in the nuclear genome of M. thibetana was found. It matched with the 3' end of the ND1 gene, the tRNA(Ile)-tRNA(Gln)-tRNA(Met) genes, the ND2 gene, and the 5' end of the tRNA(Trp) gene. Sequence divergence between the nuclear pseudogene and the mitochondrial homologue suggested that the translocation of this mtDNA fragment into the nuclear genome occurred 3.16 approximately 3.48 million years ago (MYA). Molecular phylogenetic analysis of 16 Cercopithecidae species was performed using sequences from 12 concatenated heavy-strand encoded protein coding genes. The results provided more evidence to support previous morphological and chromosomal studies on Cercopithecidae.