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Abstract The complete mitochondrial genome (mitogenome) of Periplaneta brunnea was sequenced in this study and used to reconstruct the phylogenetic relationship of Blattodea. The circular mitogenome was 15,604 bp long and exhibited typical gene organization and order, consistent with other sequenced Periplaneta mitogenomes. The initiation codon of the P. brunnea COX1 gene was unusual in that no typical ATN or TTG start codon was found. The two longest intergenic spacer sequences found in the P. brunnea mitogenome were 21 and 17 bp long. Twenty-one base spacer had a 4 bp motif (TATT) between tRNA-Glu and tRNA-Met that conservatively displayed in 9 sequenced blattarian mitogenomes. The second spacer was between tRNA-Ser ( UCN ) and NAD1 containing a 7 bp motif (WACTTAA) that was highly conserved in 14 blattarian mitogenomes. The control region showed a relatively fixed motif present in 6 Blattidae mitogenomes, with a big stem-loop structure. Phylogenetic analyses were conducted using site-homogeneous models based on 13 protein-coding genes (PCGs) and two RNA genes. The trees derived from Bayesian inference and maximum likelihood analyses and recovered a relatively stable relationship among major lineages except for the position of Polyphagidae and inter-family relationships of Blaberidae. Analyses supported the monophyly of Blattidae, Blaberidae, Blattellidae, Polyphagidae, Dictyoptera, and the paraphyly of Blattaria. We also found Mantodea was the sister clade to (Blattaria + Isoptera), being the basal position of Dictyoptera in all topologies. Meanwhile, our results also consistently supported that Isoptera should be clustered with Blattaria of Blattodea. Graphical abstract Unlabelled Image Highlights • The complete mitogenome of P. brunnea was sequenced. • The initiation codon of the P. brunnea COX 1 gene was unusual. • Two motifs were found in intergenic spacer sequences of P. brunnea mitogenome. • The control region of P. brunnea had a big stem-loop structure. • Phylogenetic inference method and dataset had effect on the position of Polyphagidae. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genomes of the Sichuan Sika deer (Cervus nippon sichuanicus) and the South China Sika deer (Cervus nippon kopschi) were determined. Their sizes were 16,429 and 16,428 base pairs, respectively. The similarity of the mitochondrial DNA genome among subspecies of the Chinese Sika deer was calculated, and the values estimated from complete nucleotide sequences and entire amino-acid sequences were 98.4–99.9% and 99.7–99.9%, respectively. Molecular phylogenetic analyses were conducted using maximum parsimony and Bayesian inference methods based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. The consensus of phylogenetic trees supported the monophyly of Moschidae, Cervidae and Bovidae, and placed Moschidae as a sister group to Cervidae/Bovidae. The relationships among Chinese Sika deer inferred from the phylogenetic analysis were inconsistent with subspecies designations and the present geographic distribution. Our complete mitochondrial genomes will be available as important and basic data for phylogenetics, breeding, genetics and conservation in Cervidae. [ABSTRACT FROM AUTHOR]

The whole mitochondrial genome of Hucho taimen was firstly sequenced and characterized. The genome is 16,833 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. Twelve protein-coding genes on the heavy strand showed that the content of A++T was higher than that of G++C, whereas the nd6 protein-coding gene on the light strand displayed an opposite pattern. We described the secondary structure of the origin of light strand (oriL) replication and found that the conserved 5′-GCCGG-3′ sequence motif is variable in H. taimen and some other salmonids. We conclude that the control region is variable in length and represents the high A++T content, compared with other mitochondrial control regions available in Salmonidae and other non-salmonids. Additionally, another interesting feature of H. taimen mitogenome is that a T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of the forest musk deer (Moschus berezovskii) was determined. Sequence analysis revealed that the organization of the mitochondrial genome in the forest musk deer was consistent with that of other reported mammals. Molecular phylogenetic analysis of the forest musk deer and 22 other species of the order Cetartiodactyla was conducted using maximum parsimony and Bayesian inference methods based on the 12 heavy-strand protein-coding genes, RNA genes and their combination. Both the consensus phylogenetic trees and the topologies test supported the monophyly of Cervidae, Bovidae and Cetancodonta, and placed Moschidae as a sister group to Cervidae/Bovidae. [ABSTRACT FROM AUTHOR]

The blue-winged minla (Minla cyanouroptera) belongs to Timaliidae, which is a near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of Minla cyanouroptera was sequenced and characterized. The genome is 17,862 bases in length (GenBank accession no. MK940810). The overall base composition of M. cyanouroptera mitogenome is 30.9% for A, 31.5% for C, 13.8% for G, and 23.8% for T. The nucleotide sequence data of 13 protein-coding genes of 12 Passeriformes species were used for phylogenetic analyses. Trees constructed by using Bayesian and maximum-likelihood methods demonstrated that Minla ignotincta was closest to M. cyanouroptera. [ABSTRACT FROM AUTHOR]

Historically, people made a mistake on species identification on musk deer from Shanxi population. In order to further confirm the species of this population, we sequenced its mitochondrial genome and conducted the species identification. Moreover, the genetic relationships among the sister species of musk deer were also investigated. The results showed that the species of musk deer from the Shanxi population was Moschus berezovskii, and M. anhuiensis was an independent species that had a very close relationship with M. berezovskii. Additionally, M. anhuiensis and M. berezovskii might have experienced a recent history of reproductive isolation. [ABSTRACT FROM AUTHOR]

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 tRNASer. Molecular data presented here provide a useful toll for helping set the stage for further studies and the molecular evolution of the mitochondrial genome. [ABSTRACT FROM AUTHOR]

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 theV. 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 andnd6genes, 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. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial genome ofMaruca testulaliswas determined (GenBank accession number KJ623250). It is 15,110 bp in length, and included 13 PCGs, 2 rRNA gens, 22 tRNA genes, and a A + T-rich region. Its gene order and orientation are identical to other crambid species. The AT-skew and GC-skew of the entire mitogenome are negative and the nucleotide composition is biased toward A + T nucleotides (80.6%). All PCGs begin with ATN codons, except for COI which is initiated by CGA. All the 22 tRAN genes can be fold into the typical clover-leaf secondary structure except for tRNAser(AGN). The 335 bp long A + T-rich region is located between srRNA and tRNAMetand contains some common features of the other lepidopterans, including the motif ATAGT followed by 14 bp poly-T stretches and a microsatellite-like (AT)11elements preceded by the ATTTA motif. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of Accipiter virgatus was determined. This mt-genome was 17,952 bp in length and consisted of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, one control region (CR) and one pseudo-control region (CCR). Phylogenetic analyses of 14,644 bp of mitochondrial DNA (12 protein-coding genes, 2 rRNAs and 22 tRNAs) revealed the phylogenetic position of Cathartidae ( Cathartes aura ) was more closer to Ciconiidae (storks) than Accipitridae. To investigate the divergence times of the CCRs in Falconiformes, detailed analyses of the noncoding regions (CR and CCR) were performed. We found the recently reported novel gene order in Falconiformes had multiple independent origins and hence cannot be used to infer phylogenetic lineages. Indeed, the molecular clock suggested the CCR in Falconidae emerged about 65.4 million years (Mya), while that in Pandionidae–Accipitridae clade emerged about 19.16 Mya. The intra-genomic homology between the noncoding regions was detected in Spilornis cheela , which supporting the duplication hypothesis. Furthermore, the structure of CCR should be featured by a region containing tandem repeats as two definitely separated clusters of tandem repeats were found. The findings presented here should be considered in future phylogenetic and evolutionary studies targeting the pseudo-control regions of all Falconiformes species. [ABSTRACT FROM AUTHOR]

Abstract: Efforts have been made to investigate the phylogeny of the family Bovidae; however, the relationships within this group still remain controversial. To further our understanding of the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and Maximum Likelihood methods. The results indicate that the basal divergence within the Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae species. The two Neotragus species (the suni and pygmy antelope) clustered with the impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus, which suggested that the Antilopinae was a paraphyletic subfamily. The present study confirmed a close relationship between the genera Capricornis and Naemorhedus while supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae. Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The very close relationship between Bison and Bos suggested that Bos and Bison should be integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope), unique genera which have sometimes been lumped together, were placed in different groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]