Showing papers in "Mitochondrial DNA in 2016"
TL;DR: SNPs in the mtDNA D-Loop were found to be valuable markers for colon cancer risk evaluation and significantly associated with an increased risk for Colon cancer.
Abstract: The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with cancer risk in a number of cancers. We investigated the colon cancer risk profile of D-Loop SNPs in a case-control study. The frequent alleles of nucleotides 73G/A, 146T/C, 195T/C, 324C/G, 16261C/T, and 16304T/C as well as the minor allele of 309C/C insert were significantly associated with an increased risk for colon cancer. In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colon cancer risk evaluation.
61 citations
TL;DR: The first complete mitochondrial genome of Scathophagidae is reported here, and both genomes contain all 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 r RNA genes, and a large control region, with conserved arrangement pattern reported in all cyclorrhaphan flies.
Abstract: The complete mitochondrial genomes of Musca domestica (Muscidae) and Scathophaga stercoraria (Scathophagidae) are circular molecules of 16,108 bp and 16,223 bp in length, respectively The first complete mitochondrial genome of Scathophagidae is reported here Both genomes contain all 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a large control region, with conserved arrangement pattern reported in all cyclorrhaphan flies All PCGs start with standard ATN codons except for the CO1 which starts with TCG in both species All PCGs terminate with the common stop codons TAA or TAG, except for the CO2 and ND5 in both species and ND4 in S stercoraria which end with a single T
48 citations
TL;DR: Recent studies indicate that the human mtDNA has a larger functional repertoire than previously believed, and suggest to reconsider the way to describe the human mitochondrial DNA as it may code for more than 13 proteins.
Abstract: The human mitochondrial (mt) DNA is commonly described as a small, maternally inherited molecule that encodes 13 protein components of the oxidative phosphorylation system and 24 structural RNAs required for their translation. However, recent studies indicate that the human mtDNA has a larger functional repertoire than previously believed. This paper briefly summarizes these studies, which suggest to reconsider our way to describe the human mitochondrial DNA as it may code for more than 13 proteins.
45 citations
TL;DR: The complete mitogenome of mangrove whipray Himantura granulata was first determined and the tRNA-Ser2 (GCU) could not form the typical clover-leafs structure for lacking the dihydrouridine arm.
Abstract: In this study, the complete mitogenome of mangrove whipray Himantura granulata was first determined. It is 17,657 bp in length and consists 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 1 putative control region with the typical gene arrangement and transcriptional orientation in vertebrates. Two start codon patterns and two stop codon patterns were found in the protein-coding genes. The tRNA-Ser2 (GCU) could not form the typical clover-leafs structure for lacking the dihydrouridine arm. The control region is 1914 bp in length with poor G (14.9%) and high A + T (59.1%) content.
44 citations
TL;DR: The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes and discriminated congeneric species without any confusion.
Abstract: DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.
41 citations
TL;DR: The nucleotide sequence data of 12 heavy-strand protein-coding genes of Apodemus draco and other 23 rodents were used for mitochondrial genome phylogenetic analyses and the monophyly of the genus Apdemus was well supported with sister to the genus Mus.
Abstract: The genus Apodemus are the most common small rodents in fields. They are also one of the best species for biogeographic study and understanding the environmental changes. In this study, the complete mitochondrial genome sequence of Apodemus draco is determined. The mitogenome is 16 220 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region, with a base composition of 35.1% A, 29.0% T, 23.8% C and 12.1% G. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Apodemus draco and other 23 rodents were used for mitochondrial genome phylogenetic analyses. The monophyly of the genus Apodemus was well supported with sister to the genus Mus. Bayesian analysis also suggested that Apodemus draco was a sister to Apodemus latronum. The present study may facilitate further investigation of the molecular evolution and biogeographic study of the genus Apodemus.
38 citations
TL;DR: The phylogenetic tree shows that Kamimuria chungnanshana is sister group of Kamimia wangi, and the complete mitochondrial genome of the stonefly is determined.
Abstract: This study determined the complete mitochondrial (mt) genome of the stonefly, Kamimuria chungnanshana Wu, 1948. The mt genome is 15, 943 bp in size and contains 37 canonical genes which include 22 transfer RNA genes, 13 protein-coding genes, and two ribosomal RNA genes, the control region is 1062 bp in length. The phylogenetic tree shows that Kamimuria chungnanshana is sister group of Kamimuria wangi.
37 citations
TL;DR: Recent global status, approaches, and future direction of DNA barcoding in fisheries sectors are investigated and barcode promotion is concluded as an indispensable tool of molecular biology for the development of taxonomic support systems.
Abstract: DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems
36 citations
TL;DR: The complete chloroplast genomes for two distinct hemp varieties of C. sativa, Italian “Carmagnola” and Russian “Dagestani”, and one Czech variety of H. lupulus are reported.
Abstract: Cannabis and Humulus are sister genera comprising the entirety of the Cannabaceae sensu stricto, including C. sativa L. (marijuana, hemp), and H. lupulus L. (hops) as two economically important crops. These two plants have been used by humans for many purposes including as a fiber, food, medicine, or inebriant in the case of C. sativa, and as a flavoring component in beer brewing in the case of H. lupulus. In this study, we report the complete chloroplast genomes for two distinct hemp varieties of C. sativa, Italian "Carmagnola" and Russian "Dagestani", and one Czech variety of H. lupulus "Saazer". Both C. sativa genomes are 153 871 bp in length, while the H. lupulus genome is 153 751 bp. The genomes from the two C. sativa varieties differ in 16 single nucleotide polymorphisms (SNPs), while the H. lupulus genome differs in 1722 SNPs from both C. sativa cultivars.
34 citations
TL;DR: dPCR enables more reliable predictors of tumor status and patient prognosis by absolute quantitation using reference normalizations and provides information with accuracy and precision which is highly reproducible and less susceptible to inhibitors than qPCR.
Abstract: Digital Polymerase Chain Reaction (dPCR) is used to quantify nucleic acids and its applications are in the detection and precise quantification of low-level pathogens, rare genetic sequences, quantification of copy number variants, rare mutations and in relative gene expressions. Here the PCR is performed in large number of reaction chambers or partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid. Results are calculated by counting amplified target sequence (positive droplets) and the number of partitions in which there is no amplification (negative droplets). The mean number of target sequences was calculated by Poisson Algorithm. Poisson correction compensates the presence of more than one copy of target gene in any droplets. The method provides information with accuracy and precision which is highly reproducible and less susceptible to inhibitors than qPCR. It has been demonstrated in studying variations in gene sequences, such as copy number variants and point mutations, distinguishing differences between expression of nearly identical alleles, assessment of clinically relevant genetic variations and it is routinely used for clonal amplification of samples for NGS methods. dPCR enables more reliable predictors of tumor status and patient prognosis by absolute quantitation using reference normalizations. Rare mitochondrial DNA deletions associated with a range of diseases and disorders as well as aging can be accurately detected with droplet digital PCR.
33 citations
TL;DR: These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws.
Abstract: Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products. Here, live juvenile eels (elvers) and dried products of sharks and rays confiscated for illegal trade were identified. Twenty out of 23 (87%) randomly selected "elvers" were identified as Anguilla bicolor pacifica and 3 (13%) samples as Anguilla marmorata. On the other hand, 4 out of 11 (36%) of the randomly selected dried samples of sharks and rays were Manta birostris. The rest of the samples were identified as Alopias pelagicus, Taeniura meyeni, Carcharhinus falciformis, Himantura fai and Mobula japonica. These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws. It is evident that the illegal trade of protected aquatic species is happening in the guise of dried or processed products thus the need to put emphasis on strengthening conservation measures. This study aims to underscore the importance of accurate species identification in such cases of illegal trade and the effectivity of DNA barcoding as a tool to do this.
TL;DR: This pioneering study on molecular identification of Philippine groupers constitutes a significant contribution to the DNA barcode library of Philippine marine fishes and to the global barcode entries in general, which can be used when dealing with grouper taxonomy, biodiversity, stock assessment and trade.
Abstract: Fish identification is generally challenging because of their unpronounced and overlapping morphological characters which is true in grouper species. In the Philippines, an updated, reliable and accurate inventory of this high value commercial groupers has not been carried out previously. Using molecular tools in the identification and inventory of fish species in the country is confined to few laboratories and experts in the country. In this study, 27 species of the Serranidae family were identified from the grouper samples collected from major fish landing sites and markets in the Philippines. The grouper species were molecularly identified using the cytochrome c oxidase I (COI) sequences for DNA barcoding. The accuracy of the inferred species-level taxonomy based on COI is supported with high similarity search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values and cohesive clustering in the Neighbor-Joining Tree. Aside from reinforcing the classical methodology of grouper identification in the country, this pioneering study on molecular identification of Philippine groupers constitutes a significant contribution to the DNA barcode library of Philippine marine fishes and to the global barcode entries in general, which can be used when dealing with grouper taxonomy, biodiversity, stock assessment and trade. The results reveal the different localities where the grouper species can be possibly sourced out in the country for trade and aquaculture purposes. Several of the grouper species are included in the IUCN Red List of Threatened Species. As a tool for conservation ecology, this study signals the implementation of sustainable fisheries management regulation to protect in particular those which are listed under the IUCN.
TL;DR: The complete mitochondrial genome of Plutella xylostella (Lepidoptera: Plutellidae) was determined and presents the typical gene organization and order for completely sequenced lepidopteran mitogenomes.
Abstract: The complete mitochondrial genome (mitogenome) of Plutella xylostella (Lepidoptera: Plutellidae) was determined (GenBank accession No. KM023645). The length of this mitogenome is 16,014 bp with 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and an A + T-rich region. It presents the typical gene organization and order for completely sequenced lepidopteran mitogenomes. The nucleotide composition of the genome is highly A + T biased, accounting for 81.48%, with a slightly positive AT skewness (0.005). All PCGs are initiated by typical ATN codons, except for the gene cox1, which uses CGA as its start codon. Some PCGs harbor TA (nad5) or incomplete termination codon T (cox1, cox2, nad2 and nad4), while others use TAA as their termination codons. The A + T-rich region is located between rrnS and trnM with a length of 888 bp.
TL;DR: The sequenced fly strains form a powerful model for mitochondrial research, when it comes to elucidating the links between the mitochondrial genotype and the phenotype, and can be used as a guide for further research into mitochondrial disease.
Abstract: The complete mitogenomes of 13 strains of the fruit fly Drosophila melanogaster were sequenced. Haplotypes varied between 19 532 and 19 537 bp in length, and followed standard dipteran mitogenome content and organization. We detected a total of 354 variable sites between all thirteen haplotypes, while single pairs of haplotypes were separated by an average of 123 variable sites. The sequenced fly strains form a powerful model for mitochondrial research, when it comes to elucidating the links between the mitochondrial genotype and the phenotype.
TL;DR: Gene synteny of Asia I is overall similar to B. afer and two other members of the B. tabaci species complex Mediterranean and New World 1, and contains the tRNA-Ser2 located between the Cytb and ND1 genes found in Mediterranean and NY1, but which is absent in B.afer.
Abstract: The complete length of the Asia I member of the Bemisia tabaci species complex mitochondrial DNA genome (mitogenome) is 15,210 bp (GenBank accession no. KJ778614) with an A-T biased nucleotide composition (A: 32.7%; T: 42.4%; G: 14.0%; C: 10.8%). The mitogenome consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA (rRNAs) and a 467 bp putative control region which also includes the A+T rich repeat region. All PCGs have an ATA (n = 8) or ATG (n = 5) start codon. Gene synteny of Asia I is overall similar to B. afer and two other members of the B. tabaci species complex Mediterranean and New World 1, and contains the tRNA-Ser2 located between the Cytb and ND1 genes found in Mediterranean and New World 1, but which is absent in B. afer. The orientation of the tRNA-Arg in Asia I is on the "plus" strand and differed from Mediterranean which is found on the "minus" strand. The Asia I mitogenome size is currently ranked the second smallest after B. afer (14,968 bp) followed by New World 1 (15,322 bp) and Mediterranean (15,632 bp).
TL;DR: This paper provided the first complete mitochondrial genome of Parasarcophaga similis for entomologists as a potential tool for application of phylogenetic analysis and forensic entomology and improved and perfect dipteran mitochondrial genomes.
Abstract: Parasarcophaga albiceps is one of the forensically important fly species which belongs to the family Sarcophagidae. In this study, we report the complete mitochondrial genome of P. albiceps to provide a supplemental data for species identification. The 14 935 bp-long mitogenome is composed of 13 protein-encoding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding AT-rich region. The permutation of the genes is in conformity with that observed in the ancestral arthropod. The overall base compositions of A, G, C and T are 39.24%, 9.70%, 14.44%, and 36.62%, respectively. Phylogenetic analysis shows the composition of the P. albiceps mitochondrial genome, which is very similar to that of another eight species of Sarcophagidae. The monophyletic branches of the phylogenetic tree reveal that complete mitochondrial genome is suitable for discrimination between these species, providing high support for separation on congeneric species. Therefore, the molecular method applied to the sarcophagid species identification is feasible. The complete mitochondrial genome of P. albiceps is supposed to make contributions to enriching the dipteran mitochondrial genomes and provide a potential tool for species identification.
TL;DR: The complete mitochondrial genome of Empoasca vitis was sequenced and the gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement.
Abstract: The complete mitochondrial genome of Empoasca vitis was sequenced. The length of the mitogenome is 15,154 bp with 78.35% AT content (GenBank accession No. KJ815009). The genome encode 37 typical mitochondrial genes including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and an A+T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. Except for cox2 using GTG as start codon, other protein-coding genes (PCGs) share the start codons ATN. Usual termination codon TAA and incomplete stop codon T are using by 13 protein-coding genes. The A+T-rich region has a length of 977 bp with the AT content high to 88.95%.
TL;DR: It is shown using straightforward phylogenetic analyses of available chiropteran sequence data that the taxonomic attribution of the reported mitogenome is erroneous and the purportedly-new complete mitochondrial genome likely belongs to the Egyptian fruit bat (R. aegyptiacus) for which a reference sequence already exists.
Abstract: Mitogenomic data are increasingly used in evolutionary biology and ecology, stressing the importance for double checking the authenticity of DNA sequences. For example, Szcześniak et al. (2013) recently published the mitochondrial genome of a bat, the Leschenault's rousette (Rousettus leschenaultii). Here we show using straightforward phylogenetic analyses of available chiropteran sequence data that the taxonomic attribution of the reported mitogenome is erroneous. The purportedly-new complete mitochondrial genome likely belongs to the Egyptian fruit bat (R. aegyptiacus) for which a reference sequence already exists. We propose that future articles reporting complete mitochondrial genome sequences should mandatorily include maximum likelihood trees inferred from (i) the standard barcoding marker for the taxon under focus, which would benefit from the massive data available in public databases, and (ii) the available mitogenomes of closely related species. We also strongly advise these trees be presented as phylograms so that all pertinent phylogenetic information is displayed in the form of a topology and its associated branch lengths. Along with compulsory information on the geographical location and origin of the specimen, these new standards should help avoiding the publication of taxonomically misidentified mitogenomes that might end up as reference sequences in public databases and re-used in subsequent meta-analyses.
TL;DR: The complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis are determined and described to reveal distinct phylogenetic relationships.
Abstract: Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.
TL;DR: The complete mitochondrial genome of Hylaeus dilatatus, the first complete mitogenome of Colletidae family, is reported, which could be used in studies of molecular systematics, conservation genetics, and stock evaluation.
Abstract: Bees are one of the most well-known and important type of pollinators in agriculture and natural ecosystems, and maintaining their diversity in nature is essential In this study, we report the complete mitochondrial genome of Hylaeus dilatatus, the first mitochondrial genome of Colletidae Its complete mtDNA sequence is 15,475 bp in length, which contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region The base composition of mtDNA is 4427% A, 4152% T, 880% C and 541% G The percentage of A + T is 8579% The first complete mitogenome of Colletidae family could be used in studies of molecular systematics, conservation genetics, and stock evaluation
TL;DR: The complete mitochondrial genome of the cotton-melon aphid, Aphis gossypii Glover, was sequenced using a combination of high-throughput sequencing, traditional PCR amplification, and Sanger sequencing to produce a genome that contains 37 typical coding genes, one non-coding AT-rich region, and a repeat region found exclusively in aphids.
Abstract: The complete mitochondrial genome of the cotton-melon aphid, Aphis gossypii Glover, was sequenced using a combination of high-throughput sequencing, traditional PCR amplification, and Sanger sequencing. The genome is 15,869 bp in length, and contains 37 typical coding genes, one non-coding AT-rich region, and a repeat region found exclusively in aphids. The base composition of the genome is A (45.4%), T (38.3%), C (10.4%), and G (5.9%). All protein coding genes start with a typical ATN initiation codon; all genes use the standard termination codon (TAA) except ND4 that ends with a single TA.
TL;DR: Sharp switches between regular and swinger replication are suggested to be due to a switch in polymerization mode of regular polymerases and the possibility of swinger-encoded information, predicted in primordial genes such as rDNA.
Abstract: Swinger DNAs are sequences whose homology with known sequences is detected only by assuming systematic exchanges between nucleotides. Nine symmetric (X Y, i.e. A C) and fourteen asymmetric (X->Y->Z, i.e. A->C->G) exchanges exist. All swinger DNA previously detected in GenBank follow the A T+C G exchange, while mitochondrial swinger RNAs distribute among different swinger types. Here different alignment criteria detect 87 additional swinger mitochondrial DNAs (86 from insects), including the first swinger gene embedded within a complete genome, corresponding to the mitochondrial 16S rDNA of the stonefly Kamimuria wangi. Other Kamimuria mt genome regions are “regular”, stressing unanswered questions on (a) swinger polymerization regulation; (b) swinger 16S rDNA functions; and (c) specificity to rDNA, in particular 16S rDNA. Sharp switches between regular and swinger replication, together with previous observations on swinger transcription, suggest that swinger replication might be due to a s...
TL;DR: The phylogenetic relationship outlined in this study is well congruent with those previously shown for the order Rosales, and the resulting tree strongly supported monophyly of Rosales.
Abstract: In this study, we determined the complete chloroplast (cp) genomes from two varieties of Cannabis sativa. The genome sizes were 153,848 bp (the Korean non-drug variety, Cheungsam) and 153,854 bp (the African variety, Yoruba Nigeria). The genome structures were identical with 131 individual genes [86 protein-coding genes (PCGs), eight rRNA, and 37 tRNA genes]. Further, except for the presence of an intron in the rps3 genes of two C. sativa varieties, the cp genomes of C. sativa had conservative features similar to that of all known species in the order Rosales. To verify the position of C. sativa within the order Rosales, we conducted phylogenetic analysis by using concatenated sequences of all PCGs from 17 complete cp genomes. The resulting tree strongly supported monophyly of Rosales. Further, the family Cannabaceae, represented by C. sativa, showed close relationship with the family Moraceae. The phylogenetic relationship outlined in our study is well congruent with those previously shown for th...
TL;DR: The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence, most promising for identification variants.
Abstract: The aim of this research is to study the mitochondria non-coding region by using Sanger sequencing technique and establish the degree of variation characteristic of a fragment. FTA® Technology (FTA™ paper DNA extraction) is utilized to extract DNA. A portion of a non-coding region encompassing positions 438 to 574 for HVIII amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column were then sequenced and detected by using the ABI 3730xL DNA analyzer. The new polymorphic positions 469 and 482 that are described in this study may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence, most promising for identification variants.
TL;DR: The complete mitochondrial genome of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374 bp, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region that has the typical gene organization and order of mitogenomes from lepidopteran insects.
Abstract: The complete mitochondrial genome (mitogenome) of Spodoptera litura (Lepidoptera: Noctuidae) was determined to be 15,374 bp (GenBank accession No. KF543065), including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A + T nucleotides (81.03%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. Four of the 13 PCGs harbor the incomplete termination codon by T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1 (AGN). The A + T-rich region of the mitogenome was 326 bp in length.
TL;DR: The complete mitochondrial genome of Dixella sp.
Abstract: In the present paper, the first complete mitochondrial genome of the family Dixidae is reported. The complete mitochondrial genome of Dixella sp. is a circular molecule of 15,574 bp in length, containing all 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (srRNA and lrRNA), and a long control region. Its gene arrangement is conserved with the ancestral gene order of Drosophila yakuba, which is considered to exhibit the ground pattern of Hexapoda mitochondrial genome. Most PCGs start with standard ATN codons, while COI uses CCG, ND1 uses TTG and ND5 uses GTG as start codons. All PCGs terminate in the common stop codons TAA, except for COII and ND5 which end with a single thymine stop codon. There is a 703 bp of the control region, located between srRNA and tRNA(lle)-tRNA(Gln)-tRNA(Met) (IQM) cluster, without conserved blocks or long tandem repeats.
TL;DR: The phylogenetic tree confirms D. nuchalis and two Cicadella species are clustered into a clade, and Cicadellidae is a monophyletic group and provides support for the sister relationship of leafhopper and treehopper.
Abstract: The complete mitochondrial genome (mitogenome) of Drabescoides nuchalis (Hemiptera: Cicadellidae) was sequenced. It is 15 309 bp in length with 75.62% (A + T) content and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes, and a non-coding region (GenBank accession no. KR349344). Gene order is identical to that of the inferred ancestral insect genome. All PCGs start with an ATN codon and terminate with TAA except ND4, which has an incomplete stop codon (T). The anticodons are identical to those of Drosophila yakuba. The phylogenetic tree confirms D. nuchalis and two Cicadellidae species are clustered into a clade, and Cicadellidae is a monophyletic group and provides support for the sister relationship of leafhopper and treehopper.
TL;DR: The mitochondrial genome sequence of Levant Region honeybee, Apis mellifera syriaca, is analyzed and presented for the public for the first time and will be useful for further phylogenetic analysis.
Abstract: The mitochondrial genome sequence of Levant Region honeybee, Apis mellifera syriaca, is analyzed and presented for the public for the first time. The genome of this honeybee is 15,428 bp in its length, containing 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition is A (42.88%), C (9.97%), G (5.85%), and T (41.3%), the percentage of A and T being higher than that of G and C. Percentage of non-ATGC characters is 0.007. All the genes are encoded on H-strand, except for four subunit genes (ND1, ND4, ND4L, and ND5), two rRNA genes and eight tRNA genes. The publication of the mitochondrial genome sequence will play a vital role in the conservation genetic projects of A. mellifera, in general, and Apis mellifera syriaca, in particular; moreover, it will be useful for further phylogenetic analysis.
TL;DR: The complete mitochondrial genome sequence of Tibetan goat is described, finding that most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA.
Abstract: The Tibetan goat (Capra hircus), a breed native to China, is adapted to cold and hypoxia. Here, we describe the complete mitochondrial genome sequence of Tibetan goat. The mitochondrial genome is 16,640 bp in length, with a base composition of 33.6% A, 26.0% C, 13.1% G and 27.3% T. It has a typical mitogenome structure, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and a non-coding control region (D-loop region). Most of the genes have ATG initiation codons, whereas ND2, ND3 and ND5 start with ATA. This genomic data provides a strating point for future phylogenetics studies.
TL;DR: The results suggested distinct impacts of natural selection and artificial selection upon the mitogenome, especially the mitochondrial signatures of adaptive evolution in wild Tibetan pigs under natural selection.
Abstract: Selection in genomic regions is prevalent in mammals; however, the effects of selection on the mitogenome are not clearly understood. We determined the complete mitochondrial DNA (mtDNA) sequences ...