Limits...
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.

Show MeSH
Relative synonymous codon usage (RSCU) for the mitochondrial proteins.The X-axis shows the codon families, while the Y-axis shows RSCU values. Absent codons are shown at the top of the columns.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4199730&req=5

pone-0110625-g004: Relative synonymous codon usage (RSCU) for the mitochondrial proteins.The X-axis shows the codon families, while the Y-axis shows RSCU values. Absent codons are shown at the top of the columns.

Mentions: The amino acid frequencies without start and stop codon are similar between the different Tetranychus mitochondrial genomes (Fig. S3). The utmost frequently used amino acids are Phe (14.61–15.26%), Leu (13.14–13.85%), Met (11.25–12.83%), Ile (10.38–11.57%), Ser (9.06–9.65%) and Asn (8.25–8.59%). The mitochondrial genome of T. malaysiensis has a slight variety in the amino acid proportion of Met (12.83%, average: 11.77%) and Ile (10.38%, average: 11.29%). The seven AT-rich codons TTT-Phe (13.31–14.35%), ATT-Ile (9.52–11.02%), TTA-Leu (10.30–10.87%), ATA-Met (10.63–12.00%), AAT-Asn (6.71–7.23%), AAA-Lys (4.52–4.84%), and TAT-Tyr (3.48–3.78%) are the most frequently used codons in the Tetranychus PCGs. The slightly low ATT codon (9.52%, average: 10.54%) and high ATA codon (12.00%, average: 11.03%) usage in the T. malaysiensis mitochondria leads to the variety in the amino acid proportion. A considerable transversion likely occurred between the codon ATT and ATA in the evolution of Tetranychus mitochondria. The Relative Synonymous Codon Usage (RSCU) in Tetranychus PCGs exhibits a similar pattern and an over-usage of A and T at the third codon positions (Fig. 4). Six codons could not be identified in the T. malaysiensis mitochondrial PCGs whereas other Tetranychus PCGs abandon only 1–4 codons. Two codons (CTG and CGC) could not be identified in the PCGs of green form of T. urticae, while only one codon (AGG) is not present in the PCGs of red form of T. urticae. Several arthropods have been reported to translate the codon AGG as lysine instead of serine in mitochondrial genetic codon [51]. However, only one AGG codon was identified in the PSGs of T. urticae green form. The other mitochondrial genomes of spider mites including P. citri and P. ulmi[13] do not use AGG codon. And it is still uncertain which amino acid does the AGG codon in spider mite's mitochondrion translate.


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)

Relative synonymous codon usage (RSCU) for the mitochondrial proteins.The X-axis shows the codon families, while the Y-axis shows RSCU values. Absent codons are shown at the top of the columns.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110625-g004: Relative synonymous codon usage (RSCU) for the mitochondrial proteins.The X-axis shows the codon families, while the Y-axis shows RSCU values. Absent codons are shown at the top of the columns.
Mentions: The amino acid frequencies without start and stop codon are similar between the different Tetranychus mitochondrial genomes (Fig. S3). The utmost frequently used amino acids are Phe (14.61–15.26%), Leu (13.14–13.85%), Met (11.25–12.83%), Ile (10.38–11.57%), Ser (9.06–9.65%) and Asn (8.25–8.59%). The mitochondrial genome of T. malaysiensis has a slight variety in the amino acid proportion of Met (12.83%, average: 11.77%) and Ile (10.38%, average: 11.29%). The seven AT-rich codons TTT-Phe (13.31–14.35%), ATT-Ile (9.52–11.02%), TTA-Leu (10.30–10.87%), ATA-Met (10.63–12.00%), AAT-Asn (6.71–7.23%), AAA-Lys (4.52–4.84%), and TAT-Tyr (3.48–3.78%) are the most frequently used codons in the Tetranychus PCGs. The slightly low ATT codon (9.52%, average: 10.54%) and high ATA codon (12.00%, average: 11.03%) usage in the T. malaysiensis mitochondria leads to the variety in the amino acid proportion. A considerable transversion likely occurred between the codon ATT and ATA in the evolution of Tetranychus mitochondria. The Relative Synonymous Codon Usage (RSCU) in Tetranychus PCGs exhibits a similar pattern and an over-usage of A and T at the third codon positions (Fig. 4). Six codons could not be identified in the T. malaysiensis mitochondrial PCGs whereas other Tetranychus PCGs abandon only 1–4 codons. Two codons (CTG and CGC) could not be identified in the PCGs of green form of T. urticae, while only one codon (AGG) is not present in the PCGs of red form of T. urticae. Several arthropods have been reported to translate the codon AGG as lysine instead of serine in mitochondrial genetic codon [51]. However, only one AGG codon was identified in the PSGs of T. urticae green form. The other mitochondrial genomes of spider mites including P. citri and P. ulmi[13] do not use AGG codon. And it is still uncertain which amino acid does the AGG codon in spider mite's mitochondrion translate.

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