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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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Mitochondrial genome maps of T. urticae (green and red forms), T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.From outer to inner, the 1st circle shows the gene map and tRNA genes are abbreviated by triple letter, with Leu1 = CUN, Leu2 = UUR, Ser1 = AGN and Ser2 = UCN. The 2nd circle shows the GC content and the 3rd shows GC skew calculated as (G−C)/(G+C). GC content and GC skew are plotted as the deviation from the average value of the entire sequence.
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pone-0110625-g001: Mitochondrial genome maps of T. urticae (green and red forms), T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.From outer to inner, the 1st circle shows the gene map and tRNA genes are abbreviated by triple letter, with Leu1 = CUN, Leu2 = UUR, Ser1 = AGN and Ser2 = UCN. The 2nd circle shows the GC content and the 3rd shows GC skew calculated as (G−C)/(G+C). GC content and GC skew are plotted as the deviation from the average value of the entire sequence.

Mentions: The mitochondrial genomes of the seven common tetranychid mites in China are typical circular DNAs (Fig. 1) with lengths of about 13,000 bp (Table S2). To our knowledge, the mitochondrial genome of T. malaysiensis is the smallest within all Acari genomes accessible in the GenBank (status March 17, 2014). The mitochondrial genome sizes of the red and green forms of T. urticae differ by 4 bp. Thirty-seven genes (13 PCGs, two rRNA genes, and 22 tRNA genes) were identified in each genome (Table S4), which is typical of presently available in metazoan mitochondrial genomes [11]. Twenty genes are encoded on the majority strand (J-strand), whereas the others are encoded on the minority strand (N-strand). The gene order is the same in all seven genomes and the same as that in Panonychus citri and P. ulmi which are in the same family as Tetranychus. However, this gene order is very different from that in other Acari and chelicerates as Yuan's [13] and Van Leeuwen's [23] reports. This suggests that the mitochondrial genome rearrangement event occurred before the divergence of Panonychus and Tetranychus.


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)

Mitochondrial genome maps of T. urticae (green and red forms), T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.From outer to inner, the 1st circle shows the gene map and tRNA genes are abbreviated by triple letter, with Leu1 = CUN, Leu2 = UUR, Ser1 = AGN and Ser2 = UCN. The 2nd circle shows the GC content and the 3rd shows GC skew calculated as (G−C)/(G+C). GC content and GC skew are plotted as the deviation from the average value of the entire sequence.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110625-g001: Mitochondrial genome maps of T. urticae (green and red forms), T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus and T. pueraricola.From outer to inner, the 1st circle shows the gene map and tRNA genes are abbreviated by triple letter, with Leu1 = CUN, Leu2 = UUR, Ser1 = AGN and Ser2 = UCN. The 2nd circle shows the GC content and the 3rd shows GC skew calculated as (G−C)/(G+C). GC content and GC skew are plotted as the deviation from the average value of the entire sequence.
Mentions: The mitochondrial genomes of the seven common tetranychid mites in China are typical circular DNAs (Fig. 1) with lengths of about 13,000 bp (Table S2). To our knowledge, the mitochondrial genome of T. malaysiensis is the smallest within all Acari genomes accessible in the GenBank (status March 17, 2014). The mitochondrial genome sizes of the red and green forms of T. urticae differ by 4 bp. Thirty-seven genes (13 PCGs, two rRNA genes, and 22 tRNA genes) were identified in each genome (Table S4), which is typical of presently available in metazoan mitochondrial genomes [11]. Twenty genes are encoded on the majority strand (J-strand), whereas the others are encoded on the minority strand (N-strand). The gene order is the same in all seven genomes and the same as that in Panonychus citri and P. ulmi which are in the same family as Tetranychus. However, this gene order is very different from that in other Acari and chelicerates as Yuan's [13] and Van Leeuwen's [23] reports. This suggests that the mitochondrial genome rearrangement event occurred before the divergence of Panonychus and Tetranychus.

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.

Show MeSH
Related in: MedlinePlus