Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 815-824 ◽  
Author(s):  
James Bruce Stewart ◽  
Andrew T Beckenbach
Keyword(s):  
Genome Sequence ◽  
Genome Rearrangement ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Genome Sequences ◽  
Mutation Pressure ◽  
Stem Loop ◽  
Mitochondrial Genomics ◽  
Directional Mutation Pressure ◽  
Mt Genome

Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16 004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families.Key words: mitochondrial genomics, directional mutation pressure, A+T-rich region, Plecoptera, stonefly.

Characterization of the complete mitochondrial genome of Setaria digitata (Nematoda: Setariidae) from China

2017 ◽  
Vol 91 (6) ◽  
pp. 772-776 ◽  
Author(s):  
G.-H. Liu ◽  
J.-Y. Li ◽  
X.-Q. Zhu
Keyword(s):  
Population Genetics ◽  
Amino Acid ◽  
Sri Lanka ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Economic Losses ◽  
Setaria Digitata ◽  
Livestock Farmers ◽  
Mt Genome

AbstractSetaria digitata is a filarial parasite that causes fatal cerebrospinal nematodiasis in goats, horses and sheep, resulting in substantial economic losses to livestock farmers. In the present study, the complete mitochondrial (mt) genome of S. digitata from China was determined, characterized and compared with that of S. digitata from Sri Lanka. The identity of the mt genomes was 98.3% between S. digitata from China and Sri Lanka, and the complete mt genome sequence of S. digitata from China was slightly shorter (25 bp) than that from Sri Lanka. For the 12 protein genes, this comparison revealed sequence differences at both the nucleotide (1.4%) and amino acid (2.2%) levels. The present study determined the complete mt genome sequence of S. digitata from China, providing novel genetic markers for the study of the population genetics and molecular epidemiology of S. digitata in animals.

Insect mitochondrial genomics: the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Hemiptera: Auchenorrhyncha: Cercopoidae)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 46-54 ◽  
Author(s):  
James Bruce Stewart ◽  
Andrew T Beckenbach
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Ribosomal Subunit ◽  
Mitochondrial Genome Sequence ◽  
Mitochondrial Genomics ◽  
Philaenus Spumarius ◽  
Complete Mitochondrial Genome Sequence ◽  
Meadow Spittlebug

We present the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Auchenorrhyncha: Cercopoidae). This contribution represents the second mitochondrial genome from the Hemiptera and the second of the three hemipteran suborders sampled. The genome is a circular molecule of 16 324 bp with a total A+T content of 77.0% and 76.7% for coding regions only. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure (Clary and Wolstenholme 1985) and the hypothesized ancestral arthropod genome arrangement (Crease 1999). Nucleotide composition and codon usage are near the means observed in other insect mitochondria sequenced to date but have a higher A+T richness compared with the other hemipteran example, the kissing bug Triatoma dimidiata (Dotson and Beard. 2001. Insect Mol. Biol. 10: 205–215). The major noncoding region (the A+T rich region or putative control region) between the small ribosomal subunit and the tRNAIle gene includes two extensive repeat regions. The first repeat region includes 19 tandem repeats of a 46-bp sequence, whereas the second contains a longer sequence (146 bp) tandemly repeated four times.Key words: mitochondrial genomics, phylogeny, molecular evolution, sequence variation, spittlebug.

Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 188-202 ◽  
Author(s):  
Stephen L. Cameron ◽  
Michael F. Whiting
Keyword(s):  
Control Region ◽  
Repeat Unit ◽  
General Characteristic ◽  
Nucleotide Composition ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stem Loop ◽  
Protein Coding ◽  
Repeat Units ◽  
Mt Genome

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.

The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

Zootaxa ◽  
2012 ◽  
Vol 3238 (1) ◽  
pp. 23 ◽  
Author(s):  
AIMIN SHI ◽  
HU LI ◽  
XIAOSHUAN BAI ◽  
XUN DAI ◽  
JIAN CHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Gene Arrangement ◽  
Entire Genome ◽  
Protein Coding ◽  
Simple Loop ◽  
Secondary Structure Models ◽  
Mt Genome

The 15528 bp long complete mitochondrial genome (mt-genome) of a flat bug, Aradacanthia heissi Bai, Zhang & Cai,was determined. The entire genome contains typical 37 genes with an A+T content of 74.7%. The gene arrangement dif-fers from that of Drosophila yakuba Burla which is considered the representative ground pattern for insect mt-genomes,as the results of inversion of tRNAIle - tRNAGln and tRNACys - tRNATrp . All protein-coding genes (PCGs) use standard initia-tion codons (methionine and isoleucine), except COI which starts with TTG. Three of the 13 PCGs harbor the incompletetermination codon. Meanwhile, opposite CG-skew tendency occurs on the nucleotide composition and codon usage andthis tendency is also reflected on the J-strand and N-strand of PCGs. All tRNAs can fold into classic clover-leaf structure,whereas the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomalRNA genes of A. heissi are predicted and similar to those proposed for other insects. The control region is located betweensrRNA and tRNAGln with 81.5% A+T content, which was the most A+T-rich region of the mt-genome and four 68 bp tan-dem repeat units were found in this region. Phylogenetic analyses of available species of Pentatomomorpha showed Ara-doidea and the Trichophora are sister groups that bolstered the mainstream hypothesis, and provide the evidence for the feasibility of mt-genome data to resolve relationships at the subfamily level in Aradidae.

The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects

Genome ◽  
2016 ◽  
Vol 59 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Qiu-Ning Liu ◽  
Xin-Yue Chai ◽  
Dan-Dan Bian ◽  
Chun-Lin Zhou ◽  
Bo-Ping Tang
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Plodia Interpunctella ◽  
Rrna Genes ◽  
Likelihood Method ◽  
Trna Genes ◽  
Cox1 Gene ◽  
Stem Loop ◽  
Lepidoptera Pyralidae ◽  
Mt Genome

The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem–loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.

scholarly journals Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plantSalix suchowensis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3148 ◽  
Author(s):  
Ning Ye ◽  
Xuelin Wang ◽  
Juan Li ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mt Genome

Willow is a widely used dioecious woody plant ofSalicaceaefamily in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence ofS. suchowensiswith the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of theS. suchowensismt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported thatSalixas a sister toPopulus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research ofS. suchowensismt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

Characterization of the complete mitochondrial genome of Ortleppascaris sinensis (Nematoda: Heterocheilidae) and comparative mitogenomic analysis of eighteen Ascaridida nematodes

2017 ◽  
Vol 92 (3) ◽  
pp. 369-378 ◽  
Author(s):  
J.H. Zhao ◽  
G.J. Tu ◽  
X.B. Wu ◽  
C.P. Li
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Molecular Ecology ◽  
Protein Coding ◽  
Intestinal Nematode ◽  
The Family ◽  
Polymerase Chain ◽  
Mt Genome

AbstractOrtleppascaris sinensis (Nematoda: Ascaridida) is a dominant intestinal nematode of the captive Chinese alligator. However, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. In this study, the complete mitochondrial (mt) genome sequence of O. sinensis was first determined using a polymerase chain reaction (PCR)-based primer-walking strategy, and this is also the first sequencing of the complete mitochondrial genome of a member of the genus Ortleppascaris. The circular mitochondrial genome (13,828 bp) of O. sinensis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes, but lacked the ATP synthetase subunit 8 gene. Finally, phylogenetic analysis of mtDNAs indicated that the genus Ortleppascaris should be attributed to the family Heterocheilidae. It is necessary to sequence more mtNDAs of Ortleppascaris nematodes in the future to test and confirm our conclusion. The complete mitochondrial genome sequence of O. sinensis reported here should contribute to molecular diagnosis, epidemiological investigations and ecological studies of O. sinensis and other related Ascaridida nematodes.

scholarly journals Complete Mitochondrial Genome Sequence ofAcrida cinerea(Acrididae: Orthoptera) and Comparative Analysis of Mitochondrial Genomes in Orthoptera

2010 ◽  
Vol 2010 ◽  
pp. 1-16 ◽  
Author(s):  
Nian Liu ◽  
Yuan Huang
Keyword(s):  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Size Variation ◽  
Nucleotide Composition ◽  
Replication Initiation ◽  
Length Variation ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Secondary Structure Models

The complete 15,599-bp mitogenome ofAcrida cinereawas determined and compared with that of the other 20 orthopterans. It displays characteristic gene content, genome organization, nucleotide composition, and codon usage found in other Caelifera mitogenomes. Comparison of 21 orthopteran sequences revealed that the tRNAs encoded by the H-strand appear more conserved than those by the L-stand. All tRNAs form the typical clover-leaf structure excepttrnS(agn), and most of the size variation among tRNAs stemmed from the length variation in the arm and loop of TΨC and the loop of DHU. The derived secondary structure models of therrnSandrrnLfrom 21 orthoptera species closely resemble those from other insects on CRW except a considerably enlarged loop of helix 1399 ofrrnSin Caelifera, which is a potentially autapomorphy of Caelifera. In the A+T-rich region, tandem repeats are not only conserved in the closely related mitogenome but also share some conserved motifs in the same subfamily. A stem-loop structure, 16 bp or longer, is likely to be involved in replication initiation in Caelifera and Grylloidea. A long T-stretch (>17 bp) with conserved stem-loop structure next torrnSon the H-strand, bounded by a purine at either end, exists in the three species from Tettigoniidae.

Sign in / Sign up

Export Citation Format

Share Document