The Complete Mitochondrial Genomes of Six Species of Tetranychus Provide Insights into the Phylogeny and Evolution of Spider Mites

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.

Ancestral reconstruction of tick lineages

“…In both these cases, N. namaqua would be incorporated into the respective families, with no resolution to their disparate lifestyle histories. Nuttalliella namaqua may also group basal to the argasid and ixodid families thereby retaining the three tick families as well as the monophyletic nature of the Ixodida, as was observed for 18S, 18S-28S rRNA and mitochondrial genome analysis (Chen et al 2014;Gu et al 2014;Mans et al 2015Mans et al , 2012Mans et al , 2011. Parsimony considerations of the latter position on the tick tree suggest a monophyletic origin for hematophagy in ticks ).…”

Next-generation sequencing as means to retrieve tick systematic markers, with the focus on Nuttalliella namaqua (Ixodoidea: Nuttalliellidae)

“…Maximum likelihood analysis using total mitochondrial nucleic acid data observed the same grouping (Gu et al 2014;Chen et al 2014). Maximum likelihood analysis using a different mitochondrial protein gene set indicated that N. namaqua grouped with the Ixodidae, while the Holothryida as sistergroup to the ticks were replaced by the Mesostigmata (Burger et al 2014).…”

“…Analysis of the nuclear 18S rRNA and mitochondrial genes indicated that N. namaqua group basal to the Argasidae and Ixodidae (Mans et al 2011;Mans et al 2012;Gu et al 2014;Chen et al 2014). Other studies using concatenated 18S-28S rRNA gene sets suggested that N. namaqua does not group basal to the other tick families, but shows a closer affinity to the Argasidae , or that its relationship to the other families was unresolved (Burger et al 2014), or that it shows a closer relationship to the Ixodidae using mitochondrial data (Burger et al 2014).…”

Development of species‐specific primers for rapid diagnosis of Tetranychus urticae, T. kanzawai, T. phaselus and T. truncatus (Acari: Tetranychidae)

“…Further, the complete mitochondrial genome was determined from six species of the genus Tetranychus (Chen et al . ). However, previous studies on the acaroid mites have indicated that ribosomal ITS2 sequences are more conserved than mitochondrial COI sequences (Navajas et al .…”