Showing papers in "Mitochondrial DNA Part B in 2017"
TL;DR: The result supported that Xylomyidae and Stratiomyidae are sister group.
Abstract: The complete mitochondrial genome (mitogenome) of Allognosta vagans (Loew, 1873) has been reported in this study. This is the first sequenced mitogenome of the subfamily Beridinae. The genome is 15...
30 citations
TL;DR: The mitochondrial genome of Ectophasia roundiventris (Loew, 1858), the first representative of subfamily Phasiinae, was sequenced and annotated and the codon ATG was the most popular start codon.
Abstract: The mitochondrial genome of Ectophasia roundiventris (Loew, 1858), the first representative of subfamily Phasiinae, was sequenced and annotated. So far, there are four Tachinidae mitochondrial genomes, here, all of them are used in Neighbour-Join and Maximum Likelihood analyses. The nucleotide composition of Ectophasia roundiventris mitochondrial genome was 40.4% of A, 39.0% of T, 11.8% of C, 8.8% of G, 79.4% of A + T content. The codon ATG was the most popular start codon. The conservative stop codon was TAA, COX2, and ND5 terminated with an incomplete stop codon T, while the gene ND4 was ended with stop codon TA.
28 citations
TL;DR: The complete mitochondrial genome of the Aster leafhopper Macrosteles quadrilineatus was sequenced using an Illumina-based next-generation sequencing approach and two tandem repeats were identified within the A + T-rich region.
Abstract: The complete mitochondrial genome of the Aster leafhopper Macrosteles quadrilineatus was sequenced using an Illumina-based next-generation sequencing approach. The genome is 16,626 bp in length with 78.0% AT content. It encodes 37 typical mitochondrial genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 A + T-rich region. Two tandem repeats were identified within the A + T-rich region. One tRNA gene rearrangement (trnW-trnC-trnY→trnC-trnW-trnY) was found between nd2 and cox1.
25 citations
TL;DR: A phylogenetic tree showed that A.m. lamarckii clusters with other A. mellifera subspecies, as expected, and all of the 22 tRNA genes, ranging from 66 to 80 bp, have a typical cloverleaf structure.
Abstract: The complete mitochondrial genome of the western honey bee subspecies Apis mellifera lamarckii was sequenced. This mitochondrial genome is 16,589 bp in length with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene directions and arrangements are similar to those of other Apis mitogenomes. Seven genes begin with ATT, four with ATG, and two with ATA (none with ATC) and all genes terminate with TAA. Four genes are encoded on the heavy strand and nine are encoded on light strand. All of the 22 tRNA genes, ranging from 66 to 80 bp, have a typical cloverleaf structure. A phylogenetic tree showed that A.m. lamarckii clusters with other A. mellifera subspecies, as expected.
22 citations
TL;DR: The complete mitochondrial genome of the western honey bee subspecies Apis mellifera meda was sequenced, with 37 classical eukaryotic mitochondrial genes and an A + T-rich region and 22 tRNA genes have a typical cloverleaf structure.
Abstract: The complete mitochondrial genome of the western honey bee subspecies Apis mellifera meda was sequenced. This mitochondrial genome is 16,248 bp in length, with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene direction and arrangement are similar to those of other Apis mitogenomes. All genes initiate with ATT (six genes), ATG (four genes), ATA (two genes), and ATC (one gene) start codons and terminate with a TAA stop codon. Four genes are encoded on the heavy and nine on the light strands, respectively. All of the 22 tRNA genes, ranging from 66 to 78 bp, have a typical cloverleaf structure. The complete mitogenome of A.m. meda provides information on the biogeography and evolution of A. mellifera subspecies.
21 citations
TL;DR: The complete mitogenome of E. onukii can provide essential DNA molecular data for further phylogenetic and evolutionary analysis and showed that it is closely related to E. vitis with high bootstrap value supported.
Abstract: Tea green leafhopper, Empoasca onukii (Hemiptera: Cicadellidae), is one of the most serious pest insects in tea plantations in Asia. In this study, Mitogenome of this species was assembled with hig...
20 citations
TL;DR: The maximum likelihood phylogenetic analysis based on 21 chloroplast genomes showed that camellia oleifera was similar to Camellia danzaiensis, and the whole genome contained a total of 115 different genes.
Abstract: Camellia oleifera, an evergreen small tree or shrub with high medicinal and ecological values, is mainly distributed in subtropical montane regions of China. In this study, complete chloroplast gen...
19 citations
TL;DR: Phylogenetic analysis places Euschemon rafflesia as a sister to the rest of Hesperiidae except Coeliadinae, and its gene order is typical for mitogenomes of Lepidoptera.
Abstract: We assembled a complete mitochondrial genome of a unique Australian skipper butterfly Euschemon rafflesia (Hesperiidae) from next generation sequencing reads. The 15,447 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Its gene order is typical for mitogenomes of Lepidoptera. Phylogenetic analysis places Euschemon rafflesia as a sister to the rest of Hesperiidae except Coeliadinae.
17 citations
TL;DR: The phylogenetic tree shows that Syrphidae is the sister group of Pipunculidae, and this is the first sequenced mitogenome from the subfamily Milesiinae.
Abstract: The complete mitochondrial genome of Eristalis tenax (Linnaeus, 1758) (Diptera, Syrphidae) is reported here. This is the first sequenced mitogenome from the subfamily Milesiinae. The whole mitochondrial genome is 16,091 bp in length and contains 37 canonical genes, which include 22 transfer RNA genes, 13 protein-coding genes and two ribosomal RNA genes, the control region is 1125 bp in length. Most PCGs start with standard ATN codons, while CO1 and ND1 use TTG, CO3 uses TGG as start codons. All PCGs terminate in the common stop codons TAA. In addition, the nucleotide composition of the coding region was 40.0% of A, 40.1% of T, 11.2% of C, 8.7% of G and 80.1% of A + T content. The phylogenetic tree shows that Syrphidae is the sister group of Pipunculidae.
16 citations
TL;DR: Of the 12 protein-coding genes (PCGs), five genes (ND1, ATP6, ND5, CO3, ND3) had incomplete stop codons and the start codon of ND4 and CO3 gene was ATA, while the startCodon of other PCGs was ATG.
Abstract: The two complete mitochondrial genomes were sequenced from the monogonont rotifer Brachionus rotundiformis. The genome sequences were 10,268 bp and 11,703 bp in size, and the gene order and contents were identical with those of B. koreanus but were different in tRNA-Cys with B. plicatilis mitochondrial genomes. Of the 12 protein-coding genes (PCGs), five genes (ND1, ATP6, ND5, CO3, ND3) had incomplete stop codons. Furthermore, the start codon of ND4 and CO3 gene was ATA, while the start codon of other PCGs was ATG. The base composition of B. rotundiformis mitogenome shows an anti-G bias (12.05% and 10.24%) on the second and third position of the PCGs, respectively.
16 citations
TL;DR: The complete chloroplast genome of M. candidum is reported, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species.
Abstract: The plant genus Melastoma is comprised of members estimated to have formed through recent species radiation. Natural hybridization among member species further complicates taxonomy within the genus. Herein, we report the complete chloroplast genome of M. candidum, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species. The chloroplast genome was 156,682 bp in length, with a large single-copy (LSC) region of 86,084 bp, a small single-copy (SSC) region of 17,094 bp, separated by two inverted repeat (IR) regions of 26,752 bp each. It was predicted to contain a total of 129 genes, with an overall GC content of 37.17%. Phylogenetic analysis placed M. candidum in the same clade as species within the Melastomeae tribe of Melastomataceae.
TL;DR: The complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa is reported, with fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
Abstract: We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9 kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
TL;DR: The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the masked shrew.
Abstract: The complete mitogenome sequence of the masked shrew (Sorex caecutiens) was determined using long PCR. The genome was 17,096 bp in length and contained 13 protein-coding genes, two ribosomal RNA ge...
TL;DR: The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of flat-skulled shrew.
Abstract: The complete mitogenome sequence of flat-skulled shrew (Sorex roboratus) was determined using long PCR. The genome was 17,153 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.1%), C (24.4%), T (29.4%), and G (13.1%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of flat-skulled shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
TL;DR: The complete mitochondrial genome of Eurydema maracandica was sequenced and was 15,391 bp long with 76.82% A++T as mentioned in this paper.
Abstract: The complete mitochondrial genome of Eurydema maracandica was sequenced and was 15,391 bp long with 76.82% A + T. There were 37 typical genes including 13 protein-coding genes/PCGs, 22 transfer RNA/tRNAs, and 2 ribosomal RNA/rRNAs. The 690 bp D-loop region was located between 12S rRNA and trnI-Ile. All PCGs started with ATN codons, except COI, ATP8, and ND1, and ended with TAA, except COI, COII, and ND5. Phylogenetic analyses indicated highly supported monophyly for each family, and Pentatomidae species formed a solid monophyletic group. Eurydema maracandica and Eurydema gebleri were clustered sibling clades, and the genus Halyomorpha was close to Eurydema.
TL;DR: The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the Ussuri shrew.
Abstract: The complete mitogenome sequence of the Ussuri shrew (Sorex mirabilis) was determined using long PCR. The genome was 17,315 bp in length and contained 13 protein-coding genes, two ribosomal RNA gen...
TL;DR: The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the slender shrew.
Abstract: The complete mitogenome sequence of the slender shrew (Sorex gracillimus) was determined using long PCR. The genome was 17,002 bp in length and contained 13 protein-coding genes, two ribosomal RNA ...
TL;DR: The mitogenome phylogeny of Aphididae suggests that M. rhois is most closely related to the eastern Asian Rhus gall aphid S. chinensis with the present sampling scheme.
Abstract: We sequenced the complete mitochondrial genome (mitogenome) for the North American Rhus gall aphid species Melaphis rhois. The mitogenome is 15,436 bp in length with a high A + T content of 82.7%, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Its gene order is identical to that of the eastern Asian species Schlechtendalia chinensis. All protein-coding genes start with a typical ATN codon and terminate with a TAA codon except COI and ND4 by a single T residue. All the tRNAs except tRNACys formed a clover-leaf secondary structure. The mitogenome phylogeny of Aphididae suggests that M. rhois is most closely related to the eastern Asian Rhus gall aphid S. chinensis with the present sampling scheme.
TL;DR: The first complete chloroplast genome sequences of Korean raspberry, oriental herbal medicinal plant of Korea, were reported in this study andylogenetic analysis suggests that R. crataegifolius is sister to R. corchorifolio, which belongs to subgenus Idaeobatus.
Abstract: The first complete chloroplast genome sequences of Korean raspberry, oriental herbal medicinal plant of Korea, were reported in this study. The genome size was 155,714 bp, composed with one pair of inverted repeats (IRs) of 25,781 bp, which were separated by one large single copy (LSC; 85,402 bp) and one small single copy (SSC; 18,750 bp). The genome contained 131 genes, coding for 86 proteins, eight ribosomal RNAs, and 37 transfer RNAs. The overall GC content was 37.1%. Phylogenetic analysis suggests that R. crataegifolius is sister to R. corchorifolius, which belongs to subgenus Idaeobatus.
TL;DR: The complete mitogenome of Anodonta cygnea is 15,613 bp long and contains the set of 37 genes, typical for invertebrate mitogenomes, in the same order and orientation as in maternally inherited genomes of other bivalves from the same subfamily.
Abstract: The complete mitogenome of Anodonta cygnea is 15,613 bp long. This compact, circular molecule contains the set of 37 genes, typical for invertebrate mitogenomes, in the same order and orientation a...
TL;DR: The phylogenetic relationship of H. illucens and its 12 related species was reconstructed to confirm the taxonomic status of the sample and the total number of nucleic acids were 15,698 bp.
Abstract: Hermetia illucens, one kind of necrophagous insects, belongs to the family Stratiomyidae (Diptera). In this study, the complete mitochondrial genome of H. illucens was investigated. The total number of nucleic acids were 15,698 bp. The genome contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The phylogenetic relationship of H. illucens and its 12 related species was reconstructed to confirm the taxonomic status of our sample.
TL;DR: Complete sequence of the mitochondrial genome (mitogenome) from G. mellonella is reported, which is comprised of 15,320 base pairs encoding 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs and an A + T rich region.
Abstract: The larva of Galleria mellonella is widely used as a model organism for in vivo toxicology and pathogenicity testing. Here, we report complete sequence of the mitochondrial genome (mitogenome) from...
TL;DR: Maximum-likelihood phylogenetic analysis with eight Solanaceae species revealed that S. berthaultii is most closely grouped with S. tuberosum.
Abstract: Solanum berthaultii is a wild species belonging to Solanaceae family. The complete chloroplast genome of S. berthaultii was constituted by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of S. berthaultii was 155,533 bp in length and consisted of 25,593 bp of a pair of inverted repeats, 18,372 bp of small single copy and 85,975 bp of large single-copy regions. 158 genes were annotated including 105 protein-coding, 45 tRNA, and 8 rRNA genes. Maximum-likelihood phylogenetic analysis with eight Solanaceae species revealed that S. berthaultii is most closely grouped with S. tuberosum.
TL;DR: The complete chloroplast genome of H. javanica was described using Illumina paired-end sequencing and the topology of the maximum-likelihood tree is consistent with topologies found in previous studies, which support the recognition ofH.Javanica as an independent species.
Abstract: Huperzia javanica (Sw.) C. Y. Yang is a valuable medical herb used for treating Alzheimer’s disease. Here, we described the complete chloroplast genome of H. javanica using Illumina paired-end sequencing. The total genome length is 154,415 bp, containing 119 unique genes, with 86 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The gene content and their order are consistent with two previously reported Huperzia genomes. The overall GC content of the chloroplast genome of H. javanica is 36.4%. The topology of our maximum-likelihood tree is consistent with topologies found in previous studies, with H. javanica sister to a clade of H. serrata and H. lucidula. We support the recognition of H. javanica as an independent species. Huperzia serrata is more closely related to H. lucidula than to H. javanica.
TL;DR: From the phylogenetic tree analysis using 25 kinds of insect mitogenome including firefly family was found that L. lateralis is the closest to the genus Aquatica.
Abstract: We will report the complete mitochondrial genome sequence of Japanese firefly ‘Heike Botaru’, Luciola lateralis (Coleoptera: Lampyridae). Total length of this mitogenome was 16,719 bp and the compo...
TL;DR: The complete mitogenome of Graphosoma rubrolineata is determined, as the first representative for the subfamily Podopinae, and strongly supported the monophyly of each of the five superfamilies within Pentatomomorpha.
Abstract: Here, we determined the complete mitogenome of Graphosoma rubrolineata, as the first representative for the subfamily Podopinae. This mitogenome is 15,633 bp long and contains 37 typical mitochondrial genes. The genome size, gene arrangement, A + T content, codon usage and secondary structures of 22 tRNAs of the G. rubrolineata mitogenome were similar to that of other sequenced pentatomoids. This mitogenome exhibited a reverse nucleotide strand bias, i.e. positive GC-skew (0.021) and negative AT-skew (−0.086). Phylogenetic analyses based on mitogenomic data strongly supported the monophyly of each of the five superfamilies within Pentatomomorpha and recognized a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). However, G. rubrolineata clustered with three Pentatominae species, suggesting that Pentatominae probably was not monophyletic, or Podopinae may not be a valid taxonomic group. The mitogenome sequence of G. rubrolineata could contribute for better und...
TL;DR: The complete mitogenome of A. nigrocincta provides essential information on the biogeography and evolution of this Asian honey bee species.
Abstract: The complete mitochondrial genome of Apis nigrocincta was sequenced. The mitochondrial genome is a circular molecule of 15,855 bp, including 37 classical eukaryotic mitochondrial regions and an A + T-rich region. Gene directions and arrangements are similar to those of other Apis mitogenomes. Most genes initiated with ATT, though ATG and ATA were also used as start codons. Twelve of 13 protein-coding genes terminated with TAA, though ND2 terminated with TAG. Four PCG genes, eight tRNAs and both rRNAs were encoded on the heavy strand while all others were encoded on the light strand (9 PCGs and 14 tRNAs). Overall, the GC content composed 15.6% of the mitogenome. All of the 22 tRNA genes, ranging from 66 to 114 bp, have a typical cloverleaf structure. A phylogenetic tree showed that A. nigrocincta clustered closest to A. cerana. The complete mitogenome of A. nigrocincta provides essential information on the biogeography and evolution of this Asian honey bee species.
TL;DR: Phylogenetic analysis using the 13 PCGs of Bactrocera species indicated that B. depressa is a sister to the sister group containing B. tau and B. cucurbitae with the highest nodal support.
Abstract: In this study, we sequenced the complete mitochondrial genome (mitogenome) of the pumpkin fruit fly, Bactrocera depressa (Diptera: Tephritidae), which is an economically damaging pest of pumpkin and turban squash. The 15,832-bp-long complete mitogenome of the species consists of a typical set of genes, with an arrangement typical of insects. Of the 13 protein-coding genes (PCGs), 12 have a typical ATN start codon, whereas the COI gene begins with TCG, which has been identified as the start codon for all Bactrocera COI genes. The 1004-bp A + T-rich region of B. depressa is the third longest, after B. minax and B. scutellata, of the Bactrocera species for which the whole mitogenome has been sequenced. Phylogenetic analysis using the 13 PCGs of Bactrocera species indicated that B. depressa is a sister to the sister group containing B. tau and B. cucurbitae with the highest nodal support (Bayesian posterior probability =1.0).
TL;DR: The complete chloroplast genome sequence of valuable ornamental tree, Camellia japonica L. (Theaceae), was determined and Phylogenetic analysis revealed the position of C.Japonica being sister to the clade containing C. crapnelliana and C. oleifera.
Abstract: The complete chloroplast genome sequence of valuable ornamental tree, Camellia japonica L. (Theaceae), was determined. The genome size was 156,971 bp in length, containing a pair of 25,798 bp inverted repeat (IR) regions, which were separated by small and large single copy regions (SSC and LSC) of 18,394 and 86,673 bp, respectively. The cp genome contained 134 genes, including 91 coding genes, six rRNA genes, and 37 tRNA genes. The overall GC content of the chloroplast genome was 37.3%. Phylogenetic analysis revealed the position of C. japonica being sister to the clade containing C. crapnelliana and C. oleifera (subgenus Camellia).
TL;DR: Phylogenetic analysis reveals that G. mangostana is a sister group of Erythroxylum novogranatense (Erystroxylaceae) with 78% bootstrap support.
Abstract: The complete plastome sequence of Garcinia mangostana L. (Clusiaceae) is completed in this study (NCBI acc. no. KX822787). This is a first complete plastome sequence from the Clusiaceae. The complete plastome size is 158,179 bp in length and consists of a large single copy of 86,458 bp and a small single copy of 17,703 bp, separated by two inverted repeats of 27,009 bp. The G. mangostana plastome shows four minor structural modifications including infA gene loss, rpl32 gene loss, ycf3 gene intron loss and a 363 bp inversion between trnV-UAC and atpE gene. The plastome contains 111 genes, of which 77 are protein-coding genes, 30 are tRNA genes and four are rRNA genes. The average A-T content of the plastome is 63.9%. A total of 110 simple sequence loci are identified from the genome. Phylogenetic analysis reveals that G. mangostana is a sister group of Erythroxylum novogranatense (Erythroxylaceae) with 78% bootstrap support.