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The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites.

Chen DS, Jin PY, Zhang KJ, Ding XL, Yang SX, Ju JF, Zhao JY, Hong XY - PLoS ONE (2014)

Bottom Line: To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared.The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans.The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China.

ABSTRACT
Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼ 84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.

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GC% vs GC-skew and AT% vs AT-skew in the 44 Acari mitochondrial genomes.Values are calculated for mitochondrial genomes of J-strands. The X-axis provides the nucleotide skew values and the Y-axis shows the nucleotide percentages.
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pone-0110625-g002: GC% vs GC-skew and AT% vs AT-skew in the 44 Acari mitochondrial genomes.Values are calculated for mitochondrial genomes of J-strands. The X-axis provides the nucleotide skew values and the Y-axis shows the nucleotide percentages.

Mentions: The J-strands of the seven mitochondrial DNAs have high A+T contents (83.4–84.5%) which are higher than those for Acariformes (about 74% without the Tetranychidae family) and Parasitiformes (about 77%) (Fig. 2). In Acari, the AT-skew of the mitochondrial genome (average 0.009±0.013) ranges from 0.279 in Unionicola parkeri to −0.253 in Dermatophagoides farina. Within the genus Tetranychus, the species with the highest AT skews in the mitochondrial DNAs are T. malaysiensis (0.056), T. phaselus (0.050) and T. ludeni (0.041). The average GC-skew of Acari mitochondrial genomes is −0.130±0.024, ranging from −0.379 in Ornithodoros moubata to 0.231 in Dermatophagoides farina. Most Acari have negative mitochondrial genome GC-skews. The exceptions are Varroa destructor (0.178), Dermatophagoides pteronyssinus (0.194), D. farinae (0.231), Phytoseiulus persimilis (0.222), P. citri (0.033) and P. ulmi (0.005). The Tetranychus species with the lowest mitochondrial DNA skews are T. ludeni (−0.072), T. phaselus (−0.072) and T. malaysiensis (−0.070). The AT- and GC-skews are quite similar in the mitochondrial genomes of the two T. urticae forms. Most metazoan species present a clear strand asymmetry, in which the J-strand is biased in favor of A and C and the N-strand is biased in favor of T and G [50]. The J-strands of the seven mitochondrial DNAs exhibit typical GC-skews, but two completed mitochondrial genomes from the genus Panonychus have positive GC-skews. It has been suggested that such reversals are caused by inversions of the A+T-rich regions and replication origin [33].


The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites.

Chen DS, Jin PY, Zhang KJ, Ding XL, Yang SX, Ju JF, Zhao JY, Hong XY - PLoS ONE (2014)

GC% vs GC-skew and AT% vs AT-skew in the 44 Acari mitochondrial genomes.Values are calculated for mitochondrial genomes of J-strands. The X-axis provides the nucleotide skew values and the Y-axis shows the nucleotide percentages.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199730&req=5

pone-0110625-g002: GC% vs GC-skew and AT% vs AT-skew in the 44 Acari mitochondrial genomes.Values are calculated for mitochondrial genomes of J-strands. The X-axis provides the nucleotide skew values and the Y-axis shows the nucleotide percentages.
Mentions: The J-strands of the seven mitochondrial DNAs have high A+T contents (83.4–84.5%) which are higher than those for Acariformes (about 74% without the Tetranychidae family) and Parasitiformes (about 77%) (Fig. 2). In Acari, the AT-skew of the mitochondrial genome (average 0.009±0.013) ranges from 0.279 in Unionicola parkeri to −0.253 in Dermatophagoides farina. Within the genus Tetranychus, the species with the highest AT skews in the mitochondrial DNAs are T. malaysiensis (0.056), T. phaselus (0.050) and T. ludeni (0.041). The average GC-skew of Acari mitochondrial genomes is −0.130±0.024, ranging from −0.379 in Ornithodoros moubata to 0.231 in Dermatophagoides farina. Most Acari have negative mitochondrial genome GC-skews. The exceptions are Varroa destructor (0.178), Dermatophagoides pteronyssinus (0.194), D. farinae (0.231), Phytoseiulus persimilis (0.222), P. citri (0.033) and P. ulmi (0.005). The Tetranychus species with the lowest mitochondrial DNA skews are T. ludeni (−0.072), T. phaselus (−0.072) and T. malaysiensis (−0.070). The AT- and GC-skews are quite similar in the mitochondrial genomes of the two T. urticae forms. Most metazoan species present a clear strand asymmetry, in which the J-strand is biased in favor of A and C and the N-strand is biased in favor of T and G [50]. The J-strands of the seven mitochondrial DNAs exhibit typical GC-skews, but two completed mitochondrial genomes from the genus Panonychus have positive GC-skews. It has been suggested that such reversals are caused by inversions of the A+T-rich regions and replication origin [33].

Bottom Line: To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared.The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans.The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China.

ABSTRACT
Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼ 84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.

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