Complete mitochondrial genome of the endangered Mary River turtle (Elusor macrurus) and low mtDNA variation across the species' range

2016 ◽  
Vol 64 (2) ◽  
pp. 117 ◽  
Author(s):  
Daniel J. Schmidt ◽  
Brittany Brockett ◽  
Thomas Espinoza ◽  
Marilyn Connell ◽  
Jane M. Hughes
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Illumina Miseq ◽  
Base Pairs ◽  
Pet Trade ◽  
Nucleotide Variability ◽  
Natural Range ◽  
Miseq Platform

Elusor macrurus is an endangered short-necked turtle restricted to the Mary River catchment in south-eastern Queensland. Shotgun sequencing of genomic DNA was used to generate a complete mitochondrial genome sequence for E. macrurus using the Illumina MiSeq platform. The mitogenome is 16 499 base pairs (bp) long with 37 genes arranged in the typical vertebrate order and a relatively short 918-bp control region, which does not feature extensive tandem repeats as observed in some turtles. Primers were designed to amplify a 1270-bp region that includes 81% of the typically hypervariable control region. Two haplotypes were detected in a sample of 22 wild-caught individuals from eight sites across its natural range. The Mary River turtle is a species with low mtDNA nucleotide variability relative to other Chelidae. The combination of a very restricted distribution and dramatic reduction in population size due to exploitation for the pet trade are the conditions likely to have led to very low mtDNA variability in this endangered species.

Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

Zootaxa ◽  
2020 ◽  
Vol 4860 (3) ◽  
pp. 401-412
Author(s):  
ZHI-TENG CHEN
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Evolutionary Rate ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Long Control Region ◽  
Trna Genes ◽  
Stem Loop ◽  
First Time

The complete mitochondrial genome (mitogenome) of Pteronarcys sachalina Klapálek was sequenced and compared with those of two other salmonflies for the first time. The mitogenome of P. sachalina was 16,180 bp in length, with an A+T content of 70.6%. The uniform set of 37 genes (13 PCGs, 22 tRNA genes and two rRNA genes) and a long control region (1431 bp) were all annotated. Most PCGs had standard ATN start codons and TAN stop codons. COX1 exhibited the highest evolutionary rate among the 13 PCGs of sequenced species of Pteronarcyidae. ND2 was truncated at the 3′ end when compared with congeners. Most tRNA genes had typical cloverleaf secondary structures, whereas the dihydrouridine (DHU) arm of trnS1 was reduced. Tandem repeats and stem-loop (SL) structures were predicted in the control region of P. sachalina. Conserved sequences were found in control regions of the three already sequenced salmonflies, P. sachalina, Pteronarcys princeps Banks, and Pteronarcella badia (Hagen). 

scholarly journals Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 724 ◽  
Author(s):  
Xiaolei Yu ◽  
Wei Tan ◽  
Huanyu Zhang ◽  
Weiling Jiang ◽  
Han Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Ground Beetle ◽  
Purifying Selection ◽  
Trna Genes ◽  
Stem Loop ◽  
Protein Coding

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

The complete mitochondrial genome of the plant bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae: Bryocorinae: Dicyphini)

Zootaxa ◽  
2012 ◽  
Vol 3554 (1) ◽  
pp. 30 ◽  
Author(s):  
XUN DAI ◽  
HUAIZHU XUN ◽  
JIAN CHANG ◽  
JIANGUO ZHANG ◽  
BAOWEN HU ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Trna Genes ◽  
Nesidiocoris Tenuis

Nesidiocoris tenuis (Reuter) is a zoophytophagous mirid which is considered both as a significant natural enemy and an important pest of crops. The complete mitochondrial genome (mitogenome) of N. tenuis was determined using long PCR and a primer walking sequencing strategy. The genome is 17, 544 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (lrRNA and srRNA), and a duplicate control region. The gene order of this newly sequenced genome is identical with the ground plan of insects. The nucleotide composition is biased toward adenine and thymine with a high AT content (75.0%). The most frequent codons are ATA, TTA, TTT, and ATT. All the PCGs initiate with the standard start codon ATN. All tRNAs have the classic cloverleaf structures, with the exception of tRNASer(UCG), which lacks the dihydrouridine (DHU) arm. Secondary structures of the two ribosomal RNAs were shown referring to previous models. Variable numbers of tandem repeats were detected in the control region. The phylogenetic analyses shows that N. tenuis is the sister group to Lygus lineolaris (Palisot de Beauvois).

The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications

Zootaxa ◽  
2020 ◽  
Vol 4747 (3) ◽  
pp. 547-561
Author(s):  
QING ZHAO ◽  
GERASIMOS CASSIS ◽  
LING ZHAO ◽  
YIFAN HE ◽  
HUFANG ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Stink Bug ◽  
Protein Coding ◽  
Simple Loop ◽  
Phylogenetic Implications ◽  
Maximum Likelihood Methods

Zicrona caerulea (Linnaeus, 1758) is a cosmopolitan stink bug species, which belongs to the predatory subfamily Asopinae. In this study, the complete mitochondrial genome of Zicrona caerulea from Shanxi, China was sequenced for the first time, using next generation sequencing. The mitogenome was found to be 15,479 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 77.14%. All tRNA genes had a clover-leaf structure except for trnS1, which lacks a dihydrouridine (DHU) arm; and for trnV, the DHU arm forms a simple loop. The lengths of rrnS and rrnL were 797 bp and 1,285 bp, respectively. Because of a shortage in tandem repeats, the A+T-rich region was 644 bp in length. Phylogenetic relationships based on these mitogenomes, using Bayesian inference and Maximum likelihood methods, showed that Zicrona caerulea belongs to Asopinae. The monophyly of families of the Pentatomoidea is supported, albeit limited taxon sampling. 

scholarly journals Unusual mtDNA Control Region Length Heteroplasmy in the COS-7 Cell Line

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 607
Author(s):  
Nataliya Kozhukhar ◽  
Sunil Mitta ◽  
Mikhail F. Alexeyev
Keyword(s):  
Mitochondrial Genome ◽  
Cell Line ◽  
Control Region ◽  
Tandem Repeats ◽  
Variable Number ◽  
Length Heteroplasmy ◽  
Repeat Units ◽  
Chlorocebus Aethiops ◽  
Region Length ◽  
Transcription And Replication

The COS-7 cell line is a workhorse of virology research. To expand this cell line’s utility and to enable studies on mitochondrial DNA (mtDNA) transcription and replication, we determined the complete nucleotide sequence of its mitochondrial genome by Sanger sequencing. In contrast to other available mtDNA sequences from Chlorocebus aethiops, the mtDNA of the COS-7 cell line was found to contain a variable number of perfect copies of a 108 bp unit tandemly repeated in the control region. We established that COS-7 cells are heteroplasmic with at least two variants being present: with four and five repeat units. The analysis of the mitochondrial genome sequences from other primates revealed that tandem repeats are absent from examined mtDNA control regions of humans and great apes, but appear in lower primates, where they are present in a homoplasmic state. To our knowledge, this is the first report of mtDNA length heteroplasmy in primates.

Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae)

Zootaxa ◽  
2019 ◽  
Vol 4550 (4) ◽  
pp. 585
Author(s):  
GAËL ALEIX-MATA ◽  
FRANCISCO J. RUIZ-RUANO ◽  
JESÚS M. PÉREZ ◽  
MATHIEU SARASA ◽  
ANTONIO SÁNCHEZ
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Tetrao Urogallus ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
Putative Origin ◽  
Fragmented Population ◽  
Galliform Bird

The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP). 

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