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Complete mitochondrial genome of the free-living earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and phylogeny of Polyneoptera.

Wan X, Kim MI, Kim MJ, Kim I - PLoS ONE (2012)

Bottom Line: We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects.The reversal pattern of skewness is explained in terms of inversion of replication origin.All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota.

View Article: PubMed Central - PubMed

Affiliation: College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea.

ABSTRACT
The insect order Dermaptera, belonging to Polyneoptera, includes ∼2,000 extant species, but no dermapteran mitochondrial genome has been sequenced. We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects. In addition, the Dermaptera, together with the other known polyneopteran mitochondrial genome sequences (protein coding, ribosomal RNA, and transfer RNA genes), were employed to understand the phylogeny of Polyneoptera, one of the least resolved insect phylogenies, with emphasis on the placement of Dermaptera. The complete mitochondrial genome of C. fletcheri presents the following several unusual features: the longest size in insects is 20,456 bp; it harbors the largest tandem repeat units (TRU) among insects; it displays T- and G-skewness on the major strand and A- and C-skewness on the minor strand, which is a reversal of the general pattern found in most insect mitochondrial genomes, and it possesses a unique gene arrangement characterized by a series of gene translocations and/or inversions. The reversal pattern of skewness is explained in terms of inversion of replication origin. All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota.

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Tandem repeat units and tRNA-like sequences found in the A+T-rich region of C. fletcheri.(A) The A+T-rich region sequence of C. fletcheri; (B) Predicted secondary structures for 3 tRNA-like sequences found in the A+T-rich region. The sequences covered by green and yellow are tandem repeat units; the single underline and double underlines indicate trnI-like and trnY-like sequences, respectively; the italic nucleotides indicate trnD-like sequences; the rectangular boxes indicate the respective anticodons, and the nucleotide position is indicated at the beginning and end sites of the sequence.
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pone-0042056-g003: Tandem repeat units and tRNA-like sequences found in the A+T-rich region of C. fletcheri.(A) The A+T-rich region sequence of C. fletcheri; (B) Predicted secondary structures for 3 tRNA-like sequences found in the A+T-rich region. The sequences covered by green and yellow are tandem repeat units; the single underline and double underlines indicate trnI-like and trnY-like sequences, respectively; the italic nucleotides indicate trnD-like sequences; the rectangular boxes indicate the respective anticodons, and the nucleotide position is indicated at the beginning and end sites of the sequence.

Mentions: The A+T-rich region of C. fletcheri is 1,816 bp long, is located between rrnS and trnM, and contains a high A/T content of 89.31% (Table S1). Such a long C. fletcheri A+T-rich region is attributable to 4 tandem repeats composed of 2 identical 297-bp copies, 2 nearly identical copies, plus a 60-bp partial copy of the beginning of the repeat (Figure 3A). Along with the tandem repeats, each of the 4 identical trnY-like, trnI-like, and trnD-like sequences were detected (Figures 3A and 3B). The sequence homology between the regular and tRNA-like sequence was 50% for trnY, 66% for trnI, and 59% for trnD, showing substantial sequence divergence between them. The long tandem repeats also have been found in several other polyneopteran A+T-rich regions, such as Mantodea, Isoptera, and Orthoptera [33]–[35]. For example, the Reticulitermes hageni (Isoptera) A+T-rich region harbored two 189-bp tandem repeats plus an 89-bp partial copy of the beginning of the repeat, and two 554-bp tandem repeats plus a 99-bp partial copy of the beginning of the repeat [34].


Complete mitochondrial genome of the free-living earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and phylogeny of Polyneoptera.

Wan X, Kim MI, Kim MJ, Kim I - PLoS ONE (2012)

Tandem repeat units and tRNA-like sequences found in the A+T-rich region of C. fletcheri.(A) The A+T-rich region sequence of C. fletcheri; (B) Predicted secondary structures for 3 tRNA-like sequences found in the A+T-rich region. The sequences covered by green and yellow are tandem repeat units; the single underline and double underlines indicate trnI-like and trnY-like sequences, respectively; the italic nucleotides indicate trnD-like sequences; the rectangular boxes indicate the respective anticodons, and the nucleotide position is indicated at the beginning and end sites of the sequence.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412835&req=5

pone-0042056-g003: Tandem repeat units and tRNA-like sequences found in the A+T-rich region of C. fletcheri.(A) The A+T-rich region sequence of C. fletcheri; (B) Predicted secondary structures for 3 tRNA-like sequences found in the A+T-rich region. The sequences covered by green and yellow are tandem repeat units; the single underline and double underlines indicate trnI-like and trnY-like sequences, respectively; the italic nucleotides indicate trnD-like sequences; the rectangular boxes indicate the respective anticodons, and the nucleotide position is indicated at the beginning and end sites of the sequence.
Mentions: The A+T-rich region of C. fletcheri is 1,816 bp long, is located between rrnS and trnM, and contains a high A/T content of 89.31% (Table S1). Such a long C. fletcheri A+T-rich region is attributable to 4 tandem repeats composed of 2 identical 297-bp copies, 2 nearly identical copies, plus a 60-bp partial copy of the beginning of the repeat (Figure 3A). Along with the tandem repeats, each of the 4 identical trnY-like, trnI-like, and trnD-like sequences were detected (Figures 3A and 3B). The sequence homology between the regular and tRNA-like sequence was 50% for trnY, 66% for trnI, and 59% for trnD, showing substantial sequence divergence between them. The long tandem repeats also have been found in several other polyneopteran A+T-rich regions, such as Mantodea, Isoptera, and Orthoptera [33]–[35]. For example, the Reticulitermes hageni (Isoptera) A+T-rich region harbored two 189-bp tandem repeats plus an 89-bp partial copy of the beginning of the repeat, and two 554-bp tandem repeats plus a 99-bp partial copy of the beginning of the repeat [34].

Bottom Line: We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects.The reversal pattern of skewness is explained in terms of inversion of replication origin.All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota.

View Article: PubMed Central - PubMed

Affiliation: College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea.

ABSTRACT
The insect order Dermaptera, belonging to Polyneoptera, includes ∼2,000 extant species, but no dermapteran mitochondrial genome has been sequenced. We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects. In addition, the Dermaptera, together with the other known polyneopteran mitochondrial genome sequences (protein coding, ribosomal RNA, and transfer RNA genes), were employed to understand the phylogeny of Polyneoptera, one of the least resolved insect phylogenies, with emphasis on the placement of Dermaptera. The complete mitochondrial genome of C. fletcheri presents the following several unusual features: the longest size in insects is 20,456 bp; it harbors the largest tandem repeat units (TRU) among insects; it displays T- and G-skewness on the major strand and A- and C-skewness on the minor strand, which is a reversal of the general pattern found in most insect mitochondrial genomes, and it possesses a unique gene arrangement characterized by a series of gene translocations and/or inversions. The reversal pattern of skewness is explained in terms of inversion of replication origin. All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota.

Show MeSH
Related in: MedlinePlus