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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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Different evolutionary patterns among protein coding genes of T. urticae green form, T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.Sub./Site, the number of nucleotide substitutions per site from averaging over all sequence pairs, was calculated with JC model. Syn.Subs./Syn.Site, the number of synonymous substitutions per synonymous site (Ks); Non.Subs./Non.Site, the number of nonsynonymous substitutions per nonsynonymous site (Ka); Ks-Ka, the value of Ks minus Ka; the analysis were estimated with Kumar model [68]. The rate variation among sites was modelled with a gamma distribution calculated by Mega ver. 6 and the standard error estimations were obtained by bootstrapping 1000 replicates. Substitution rate is shown on the left Y-axis and G+C content is shown on the right Y-axis.
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pone-0110625-g005: Different evolutionary patterns among protein coding genes of T. urticae green form, T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.Sub./Site, the number of nucleotide substitutions per site from averaging over all sequence pairs, was calculated with JC model. Syn.Subs./Syn.Site, the number of synonymous substitutions per synonymous site (Ks); Non.Subs./Non.Site, the number of nonsynonymous substitutions per nonsynonymous site (Ka); Ks-Ka, the value of Ks minus Ka; the analysis were estimated with Kumar model [68]. The rate variation among sites was modelled with a gamma distribution calculated by Mega ver. 6 and the standard error estimations were obtained by bootstrapping 1000 replicates. Substitution rate is shown on the left Y-axis and G+C content is shown on the right Y-axis.

Mentions: The evolutionary patterns of the PCGs are different (Fig. 5). The cox1 gene is commonly used as a taxon barcode because of its high rates of interspecific sequence change and constraints on intraspecific divergence [52], [53]. But this gene exhibits the lowest nucleotide substitution rate per site (0.208±0.014) and lowest value of nonsynonymous substitutions per nonsynonymous site (Ka) (0.04±0.004) compared to the other genes. The nucleotide substitution rate per site (0.555±0.097) and the number of synonymous substitutions per synonymous site (Ks) (1.098±0.143) of nad3 gene are highest, while the Ka number of atp8 is highest (0.315±0.062). In addition, the GC content was found to be negatively correlated with both the nucleotide substitution rate per site (R = −0.637, P = 0.019) and Ka (R = −0.715, P = 0.006), while the nucleotide substitution rate per site was found to be positively correlated with Ka (R = 0.825, P = 0.001). Ks was not found to be associated with Ka, GC content or nucleotide substitution rate per site.


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)

Different evolutionary patterns among protein coding genes of T. urticae green form, T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.Sub./Site, the number of nucleotide substitutions per site from averaging over all sequence pairs, was calculated with JC model. Syn.Subs./Syn.Site, the number of synonymous substitutions per synonymous site (Ks); Non.Subs./Non.Site, the number of nonsynonymous substitutions per nonsynonymous site (Ka); Ks-Ka, the value of Ks minus Ka; the analysis were estimated with Kumar model [68]. The rate variation among sites was modelled with a gamma distribution calculated by Mega ver. 6 and the standard error estimations were obtained by bootstrapping 1000 replicates. Substitution rate is shown on the left Y-axis and G+C content is shown on the right Y-axis.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110625-g005: Different evolutionary patterns among protein coding genes of T. urticae green form, T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.Sub./Site, the number of nucleotide substitutions per site from averaging over all sequence pairs, was calculated with JC model. Syn.Subs./Syn.Site, the number of synonymous substitutions per synonymous site (Ks); Non.Subs./Non.Site, the number of nonsynonymous substitutions per nonsynonymous site (Ka); Ks-Ka, the value of Ks minus Ka; the analysis were estimated with Kumar model [68]. The rate variation among sites was modelled with a gamma distribution calculated by Mega ver. 6 and the standard error estimations were obtained by bootstrapping 1000 replicates. Substitution rate is shown on the left Y-axis and G+C content is shown on the right Y-axis.
Mentions: The evolutionary patterns of the PCGs are different (Fig. 5). The cox1 gene is commonly used as a taxon barcode because of its high rates of interspecific sequence change and constraints on intraspecific divergence [52], [53]. But this gene exhibits the lowest nucleotide substitution rate per site (0.208±0.014) and lowest value of nonsynonymous substitutions per nonsynonymous site (Ka) (0.04±0.004) compared to the other genes. The nucleotide substitution rate per site (0.555±0.097) and the number of synonymous substitutions per synonymous site (Ks) (1.098±0.143) of nad3 gene are highest, while the Ka number of atp8 is highest (0.315±0.062). In addition, the GC content was found to be negatively correlated with both the nucleotide substitution rate per site (R = −0.637, P = 0.019) and Ka (R = −0.715, P = 0.006), while the nucleotide substitution rate per site was found to be positively correlated with Ka (R = 0.825, P = 0.001). Ks was not found to be associated with Ka, GC content or nucleotide substitution rate per site.

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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