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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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Phylogenetic tree of Acariformes relationships.The tree was inferred from amino acid datasets and rooted with Parasitiformes taxa. Numbers at nodes are percentages from Bayesian posterior probabilities (left), ML bootstrapping (middle) and MP bootstrap support values (right). The nodes that did not support Bayesian inference or had low bootstrap support values were marked as midlines.
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pone-0110625-g006: Phylogenetic tree of Acariformes relationships.The tree was inferred from amino acid datasets and rooted with Parasitiformes taxa. Numbers at nodes are percentages from Bayesian posterior probabilities (left), ML bootstrapping (middle) and MP bootstrap support values (right). The nodes that did not support Bayesian inference or had low bootstrap support values were marked as midlines.

Mentions: Maximum-parsimony (MP), Maximum-Likelihood (ML) and Bayesian inference (BI) phylogenetic trees were constructed based on the concatenated amino acid sequences of the 13 PCGs of the seven Tetranychus species and other Acariformes. The three trees had identical topologies (Fig. 6). Almost all nodes were well supported, whereas the split between T. phaselus and the other Tetranychus species was not supported by the MP tree. The three species of Sarcoptiformes were monophyletic and clustered as a sister group of Trombidiformes, in agreement with a previous analysis [16]. The superfamily Tetranychoidea, which is considered as a member of Trombidiformes, split as a single clade and formed a sister group to other species of Trombidiformes. Another study [16] obtained a similar topology, except that the bootstrap values and BI posterior probabilities for the Tetranychoidea were low. Mitochondrial genomes evolve at high rates. It has been suggested that the three most important factors are rearrangements in the mitochondrial genome, a parasitic lifestyle and small body size [60]. Most species of Acariformes exhibit all three factors and the great variability in branch lengths suggest a high heterogeneous substitution rate among the mt genomes. These problems led to markedly long branches, and the superabundant phylogenetic signals probably led to the distant phylogenetic position of the Tetranychoidea. Identical topologies were constructed by the three approaches with high bootstrap values and high Bayesian posterior probabilities for the position of Tetranychoidea. However, additional mt genome data or trees based on more conserved sequences are needed to improve the phylogeny of Acariformes.


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)

Phylogenetic tree of Acariformes relationships.The tree was inferred from amino acid datasets and rooted with Parasitiformes taxa. Numbers at nodes are percentages from Bayesian posterior probabilities (left), ML bootstrapping (middle) and MP bootstrap support values (right). The nodes that did not support Bayesian inference or had low bootstrap support values were marked as midlines.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110625-g006: Phylogenetic tree of Acariformes relationships.The tree was inferred from amino acid datasets and rooted with Parasitiformes taxa. Numbers at nodes are percentages from Bayesian posterior probabilities (left), ML bootstrapping (middle) and MP bootstrap support values (right). The nodes that did not support Bayesian inference or had low bootstrap support values were marked as midlines.
Mentions: Maximum-parsimony (MP), Maximum-Likelihood (ML) and Bayesian inference (BI) phylogenetic trees were constructed based on the concatenated amino acid sequences of the 13 PCGs of the seven Tetranychus species and other Acariformes. The three trees had identical topologies (Fig. 6). Almost all nodes were well supported, whereas the split between T. phaselus and the other Tetranychus species was not supported by the MP tree. The three species of Sarcoptiformes were monophyletic and clustered as a sister group of Trombidiformes, in agreement with a previous analysis [16]. The superfamily Tetranychoidea, which is considered as a member of Trombidiformes, split as a single clade and formed a sister group to other species of Trombidiformes. Another study [16] obtained a similar topology, except that the bootstrap values and BI posterior probabilities for the Tetranychoidea were low. Mitochondrial genomes evolve at high rates. It has been suggested that the three most important factors are rearrangements in the mitochondrial genome, a parasitic lifestyle and small body size [60]. Most species of Acariformes exhibit all three factors and the great variability in branch lengths suggest a high heterogeneous substitution rate among the mt genomes. These problems led to markedly long branches, and the superabundant phylogenetic signals probably led to the distant phylogenetic position of the Tetranychoidea. Identical topologies were constructed by the three approaches with high bootstrap values and high Bayesian posterior probabilities for the position of Tetranychoidea. However, additional mt genome data or trees based on more conserved sequences are needed to improve the phylogeny of Acariformes.

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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