The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.

Spider mites are difficult to identify because they are very small and have a limited number of diagnostic characters. Most species of the spider mite genus Tetranychus in Japan are morphologically similar, differing only in the diameter of the aedeagal knob in males. Because this genus contains many important pests, the unambiguous identification of species is crucial for effective pest management and quarantine procedures. DNA-based methods could complement the morphological methods. We examined whether Tetranychus species in Japan could be identified by DNA sequences using the internal transcribed spacer region of nuclear ribosomal DNA and the cytochrome c oxidase subunit I gene of mitochondrial DNA. We determined sequences of the 13 known Tetranychus species in Japan. We could identify 10 of the 13 species in the internal transcribed spacer tree. In the cytochrome c oxidase subunit I tree, we could identify all 13 known Tetranychus species in Japan. Although Tetranychus kanzawai Kishida and T. parakanzawai Ehara were identified by DNA sequences, they were clearly separated into two monophyletic clades each, indicating that a cryptic species existed in each species.

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The genus Oligonychus has been morphologically divided into two groups based on the direction of curvature of the aedeagus and includes some morphologically similar species that are difficult to distinguish. To develop DNA-based methods for identifying Oligonychus species and to determine the phylogenetic relationships among them, we examined the cytochrome c oxidase subunit I gene of mitochondrial DNA and the internal transcribed spacer and 28S regions of nuclear ribosomal RNA gene for 17 species. Based on the genetic distances (p-distances) of the three DNA regions, the range of intraspecific divergence was found to be below (and not overlap) the range of interspecific divergence, which allowed the 17 species to be discriminated correctly, consistent with their classification based on morphology. Phylogenetic trees constructed by neighbor-joining and Bayesian methods clearly showed two clades, consisting of species whose aedeagi curve ventrally and dorsally, respectively. Three Oligonychus species inhabiting gramineous plants formed clearly defined subclades.

The complete genome of pepper vein yellows virus (PeVYV) was sequenced using random amplification of RNA samples isolated from vector insects (Aphis gossypii) that had been given access to PeVYV-infected plants. The PeVYV genome consisted of 6244 nucleotides and had a genomic organization characteristic of members of the genus Polerovirus. PeVYV had highest amino acid sequence identities in ORF0 to ORF3 (75.9 - 91.9%) with tobacco vein distorting polerovirus, with which it was only 25.1% identical in ORF5. These sequence comparisons and previously studied biological properties indicate that PeVYV is a distinctly different virus and belongs to a new species of the genus Polerovirus.