The complete mitochondrial genome sequence of Geisha distinctissima （Hemiptera： Flatidae） and comparison with other hemipteran insects

The complete nucleotide sequence of the mitochondrial genome （mitogenome） of Geisha distinctissima （Hemiptera： Flatidae） has been determined in this study. The genome is a circular molecule of 15,971 bp with a total A＋T content of 75.1%. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure and the hypothesized ancestral arthro- pod genome arrangement. All 13 protein-coding genes are observed to have a putative, inframe ATR methionine or ATT isoleucine codons as start signals. Canonical TAA and TAG termination codons are found in nine protein-coding genes, and the remaining four （cox1, atp6, cox3, and nad4） have incomplete termination codons. The anticodons of all transfer RNA （tRNAs） are identical to those observed in D. yakuba and Philaenus spumarius, and can be folded in the form of a typical clover-leaf structure except for tRNASer（AGN）. The major non-coding region （the A ＋ T-rich region or putative control region） between the small ribosomal subunit and the tRNAne gene includes two sets of repeat regions. The first repeat region consists of a direct 152-bp repetitive unit located near the srRNA gene end, and the second repeat region is composed of a direct repeat unit of 19 bp located toward tRNAIle gene. Comparisons of gene variability across the order suggest that the gene content and arrangement of G. distinctissima mitogenome are similar to other hemipteran insects.     

The first mitochondrial genome for the butterfly family Riodinidae(Abisara fylloides) and its systematic implications

The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A. fylloides is 15 301 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22transfer RNA genes and a 423 bp A+T-rich region. The gene content, orientation and order are identical to the majority of other lepidopteran insects. Phylogenetic reconstruction was conducted using the concatenated 13 protein-coding gene(PCG) sequences of19 available butterfly species covering all the five butterfly families(Papilionidae, Nymphalidae, Peridae, Lycaenidae and Riodinidae). Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae,which was standing as the sister of Nymphalidae. In addition, we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.     

The complete mitochondrial genome and phylogenetic analysis of Nyctereutes procyonoides

The complete mitochondrial genome sequence of the raccoon dog (Nyctereutes procyonoides) was determined by using the long and accurate polymerase chain reaction. The entire mitochondrial genome sequence is 16,713 bp in length contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 control region. Most mitochondrial genes are encoded on the H strand, except for the ND6 gene and 8 tRNA genes. The base compositions of mitochondrial genomes present clearly A–T skew. All the transfer RNA genes can be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacks the dihydrouridine arm. Protein-coding genes mainly initiate with ATG and terminate with TAA. Some reading frame intervals and overlaps are found in the mitochondrial genome. The control region can be divided into three domains: the extended termination associated sequences (ETASs) domain, the central conserved domain and the conserved sequence blocks (CSBs) domain. Three conserved sequence blocks (CSBs) and one extended termination associated sequences (ETAS-1) is found in the control region. The phylogenetic analysis based on the concatenated data set of 14 genes in the mitochondrial genome of Canidae shows that the raccoon dog has close phylogenetic position with the red fox (Vulpes vulpes) and they constitute a clade which has an equil evolutionary position with the clade formed by the genera Canis and Cuon.     

Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

The so-called ＂wild abortive＂ （WA） type of cytoplasmic male sterility （CMS） derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene（s） remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondriai genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondriai expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nad5 and orf153 genes and the other having the ribosomal protein gene rpl5, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.     

Complete mitochondrial genome of Oxya chinensis （Orthoptera, Acridoidea）

The complete sequence of Oxya chinensis （0. chinensis） mitochondrial genome is reported here. It is 15,443 bp in length and contains 75.9% A＋T. The protein-coding genes have a similar A＋T content （75.2%）. The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O. chinensis appears to be ATC, instead of the tetranucleotides that have been reported in Locusta migratoria （L migratoria） mitochondrial genome. The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp, respectively. The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs, and all anticodons are identical to those of dipteran. The A＋T-rich region is 562 bp, shorter than that of other known Orthoptera insects. The six conserved domains were identified within the A＋T-rich region by comparing its sequence with those of other grasshoppers. The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relation-ship of O. chinensis with L migratoria.     

The mitochondrial genome of the plant bug Apolygus lucorum （Hemiptera： Miridae）＂ Presently known as the smallest in Heteroptera

The complete mitochondrial （mt） genome of the plant bug, Apolygus lucorum, an important cotton pest, has been sequenced and annotated in this study. The entire circular genome is 14 768 bp in size and represents the smallest in presently known heteropteran mt genomes. The mt genome is encoding for two ribosomal RNA （rRNA） genes, 22 transfer RNA （tRNA） genes, 13 protein coding genes and a control region, and the order, content, codon usage and base organization show similarity to a great extent to the hypothetical ancestral model. All protein coding genes use standard initiation codons ATN. Conventional stop codons TAA and TAG have been assigned to the most protein coding genes; however, COIII, ND4 and ND5 genes show incomplete terminator signal （T）. All tRNA genes possess the typical clover leaf structure, but the dihydrouridine arm of tRNAser（A6N） only forms a simple loop. Secondary structure models of rRNA genes are generally in accordance with the former models, although some differences exist in certain parts. Three intergenic spacers have never been found in sequenced mt genomes of Heteroptera. The phylogenetic study based on protein coding genes is largely congruent with previous phylogenetic work. Both Bayesian inference and maximum likelihood analyses highly support the sister relationship ofA. lucorum and Lygus lineolaris, and Miridae presents a sister position to Anthocoridae.     

The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly,Artogeia melete （Lepidoptera： Pieridae）

The complete mitochondrial genome （mitogenome） of Artogeia melete was determined as being composed of 15,140 bp, including 13 protein-coding genes （PCGs）, 2 rRNA genes, 22 tRNA genes, and one control region. The gene order of A. melete mitogenome is typical of Lepidoptera and differs from the insect ancestral type in the location of trnM. The A. melete mitogenome has a total of 119 bp of intergenic spacer sequences spread over 10 regions, ranging in sizes between 1 and 48 bp. The nucleotide composition of the A. melete mitogenome is also biased toward A ＋ T nucleotides （79.77%）, which is higher than that of Ochrogaster lunifer （77.84%）, but lower than nine other lepidopterans sequenced. The PCGs have typical mitochondrial start codons, except for coxl, which contains the unusual CGA. The coxl, cox2, nad2, and nad5 genes of the A. melete mitogenome have incomplete stop codons （T）. The A. melete A ＋ T-rich region contains some conserved structures that are similar to those found in other lepidopteran mitogenomes, including a structure combining the motif ‘ATAGA＇, a 19-bp poly（T） stretch, a microsatellite （AT）n element, and a 9-bp poly（A） upstream trnM. The A. melete mitogenome contains a duplicated 36-bp repeat element, which consists of a 26- bp core sequence flanked by 10-bp perfectly inverted repeats.     

Complete mitochondrial genome of the leaf muntjac (Muntiacus putaoensis) and phylogenetics of the genus Muntiacus

The leaf muntjac (Muntiacus putaoensis) is an endemic deer species found in the east transHimalayan region.In recent years,population numbers have decreased due to heavy hunting and habitat loss,and little genetic data exists for this species,thus our knowledge of distribution rangs and population sizes likewise remain limited.We obtained mtDNA genes and the complete mitochondrial genome sequence of M.putaoensis using PCR,followed by direct sequencing.The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome,containing 13 protein-coding genes,two rRNA genes,22 tRNA genes,and one control region,the gene composition and order of which were similar to most other vertebrates so far reported.Most mitochondrial genes,except for ND6 and eight tRNAs,were encoded on the heavy strand.The overall base composition of the heavy strand was 33.1％ A,29.3％ T,24.2％ C,and 13.4％ G,with a strong AT bias of 62.4％.There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp.Phylogenetic analyses (ML and BI) among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M.putaoensis as a member of Muntiacus,most closely related to M.vuquangensis.However,when analyses based on cyt b included two more muntjacs,M.truongsonensis was most closely related to M.putaoensis rather than M.vuquangensis,and together with M.rooseveltorum,likely forming a M.rooseveltorum complex of the species.This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac,as well as its protection as a genetic resource.     

A Mitochondrial Genome Sequence of the Tibetan Antelope （ Pantholops hodgsonii ）

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis ames and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii （16,498 bp） revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. ames and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. ames and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. ames is about 2.25 million years ago. Eutther analysis on natural selection indicated that the COXI （cytochrome c oxidase subunit I） gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.     

The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorga-nization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other re-ported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non- conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.     

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis(Aves,Passeridae) complete mitochondrial genome

In this study,both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome(KC836121).The results showed that the complete mitochondrial genome of P.ruficollis is 16909 bp in length with 55.0%A+T content,harboring the typical 37 genes.The mitogenome had the same gene order with that of Podoces hendersoni.All protein coding genes started with ATG codon,except ND3 with GTG.For the stop codon usage,most genes terminate with codons TAA or TAG,but ND5 terminated with AGA,while ND1 and COI genes with AGG,and both the genes COIII and ND4 have an incomplete termination codon(T).The secondary structures of 22 tRNA genes were also predicted,showing that all tRNAs can form typical clover-leaf secondary structures,except for the tRNASer(AGN)which loses the DHU arm,while tRNAPhe harbor an extra nucleotide inserted in the TψC arm.The predicted secondary structures of 12S rRNA and16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively.The control region of P.ruficollis with the length of 1 305 bp was located between tRNAGlu and tRNAPhe,and typical domains of which could be found as other bird groups.Using the data from 13 mitochondrial protein-coding genes,results of a final phylogenetic analysis strongly supports the traditional view that P.ruficollis is closely related with Passeridae and Fringillidae.     

Complete mitochondrial genome of the Thai Red Junglefowl(Gallus gallus) and phylogenetic analysis

正DEAR EDITOR,In this study,we sequenced the complete mitochondrial genome(mitogenome)of the Thai Red Junglefowl(RJF;Gallus gallus)using the next-generation sequencing(NGS)platform of the Ion Torrent PGM.Samples were taken from Mae Wang District,Chiang Mai Province,northern Thailand.Our data showed the complete mitogenome to be 16 785bp in length,composed by 13 protein-coding genes,22tRNA genes,two rRNA genes,and one control region.The genome nucleotide composition was 30.3%A,23.7%T,32.5%C,and 13.5%G,resulting in a high percentage of A+T     

Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus)

DEAR EDITOR, In this study,we sequenced the complete mitochondrial DNA genome (mitogenome) of the Zhengyang Yellow chicken (Gallus gallus domesticus) by next-generation sequencing technology.Samples were taken from Zhumadian city,Henan Province,China.The complete mitogenome was 16 785 bp in size,and had a nucleotide composition of 30.3％ (A),23.7％ (T),32.5％ (C),and 13.5％ (G),with a high AT content of 54.0％.The assembled mitogenome exhibited typical mitochondrial DNA (mtDNA) structure,including a non-coding control region,two rRNA genes,13 protein-coding genes,and 22 tRNA genes.Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B.These results should provide essential information for chicken domestication and insight into the evolution of genomes.     

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.     

Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bomyx mandarina (Lepidoptera: Bombycidae)

The complete mitochondrial genome of Chinese Bombyx mandarina(ChBm) was determined.The cir-cular genome is 15682 bp long, and contains a typical gene complement, order, and arrangement iden-tical to that of Bombyx mori(B.mori) and Japanese Bombyx mandarina(JaBm) except for two addi-tional tRNA-like structures:tRNASer(TGA)-like and tRNAIle(TAT)-like.All protein-coding sequences are initi-ated with a typical ATN codon except for the COI gene, which has a 4-bp TTAG putative initiator codon.Eleven of 13 protein-coding genes(PCGs) have a complete termination codon(all TAA), but the re-maining two genes terminate with incomplete codons.All tRNAs have the typical clover-leaf structures of mitochondrial tRNAs, with the exception of tRNASer(TGA)-like, with a four stem-and-loop structure.The length of the A T-rich region of ChBm is 484 bp, shorter than those of JaBm(747 bp) and B.mori(494―499 bp).Phylogenetic analysis among B.mori, ChBm, JaBm, and Antheraea pernyi(Anpe) showed that B.mori is more closely related to ChBm than JaBm.The earliest divergence time estimate for B.mori-ChBm and B.mori-JaBm is about 1.08±0.18―1.41±0.24 and 1.53±0.20―2.01±0.26 Mya, respec-tively.ChBm and JaBm diverged around 1.11±0.16―1.45±0.21 Mya.     

Phylogenetic placement of Cynomorium in Rosales inferred from sequences of the inverted repeat region of the chloroplast genome

Cynomorium is a herbaceous holoparasite that has been placed in Santalales, Saxifragales, Myrtales, or Sapindales. The inverted repeat （IR） region of the chloroplast genome region is slow evolving and, unlike mitochondrial genes, the chloroplast genome experiences few horizontal gene transfers between the host and parasite. Thus, in the present study, we used sequences of the IR region to test the phylogenetic placements of Cynomorium. Phylogenetic analyses of the chloroplast IR sequences generated largely congruent ordinal relationships with those from previous studies of angiosperm phylogeny based on single or multiple genes. Santalales was closely related to Caryophyllales and asterids. Saxifragales formed a clade where Peridiscus was sister to the remainder of the order, whereas Paeonia was sister to the woody clade of Saxifragales. Cynomorium is not closely related to Santalales, Saxifragales, Myrtales, or Sapindales; instead, it is included in Rosales and sister to Rosaceae. The various placements of the holoparasite on the basis of different regions of the mitochondrial genome may indicate the heterogeneous nature of the genome in the parasite. However, it is unlikely that the placement of Cynomorium in Rosales is the result of chloroplast gene transfer because Cynomorium does not parasitize on rosaceous plants and there is no chloroplast gene transfer between Cynomorium and Nitraria, a confirmed host of Cynomorium and a member of Sapindales.     

Bioinformatic identification of genes encoding Clq-domaincontaining proteins in zebrafish

C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular （gC1q） domain similar with C1q was also found in many non-complement C1q-domain-containing （C1qDC） proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor （TNF） ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing （C1qDC） proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.     

Phylogenetic Analysis of Brine Shrimp （Artemia） in China Using DNA Barcodinge

DNA barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 （COI）, as a standard barcode region to establish phylogenetic relationships among brine shrimp （Artemia） species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.