Norihide Hinomoto

Genetic diversity and phylogeny of the Kanzawa spider mite, Tetranychus kanzawai, in Japan

Two types are known in the Kanzawa spider mite, Tetranychus kanzawai (K and T; see Gotoh et al., 1999), which differ in host range and have a unidirectional incompatibility. Prior to DNA analyzes, crossing between females of a known K type and males of each of 17 strains collected in Japan showed that six of the strains were of the K type, five were the T type and the rest consisted of a mixture of the two types. In order to elucidate the genetic diversity and phylogenetic relationship of T. kanzawai in Japan, we analyzed the DNA sequences of two regions – the internal transcribed spacer 1 (ITS1) of the nuclear ribosomal DNA (rDNA) and a fragment of the cytochrome oxidase subunit I gene (COI) of mitochondrial DNA – using 11 strains (six K-type strains and five T-type strains). Base substitutions were detected on 25 sites of COI (375 bp) and 19 sites of ITS1 (486 bp), resulting in eight and 17 haplotypes, respectively. The phylogenetic trees constructed using the DNA sequences failed to clearly distinguish between the two types. The results suggested that the T type was derived from the K type.

Identification of spider mites (Acari: Tetranychidae) by DNA sequences: A case study in northern Vietnam

Abstract Identification of spider mite species has been an important but complicated issue in pest control. We studied the species composition of spider mites collected in agricultural fields of northern Vietnam by using mitochondrial cytochrome oxidase subunit I sequences as a case study of the DNA barcoding identification technique for spider mites. Specimens were identified by comparing obtained DNA sequences with known sequences deposited in DNA databases. If phylogenetic analysis was used together, the DNA barcoding approach was useful for species identification of spider mites, especially for the genus Tetranychus. Using DNA barcoding, we classified most of the Vietnamese samples into Tetranychus kanzawai Kishida, T. urticae Koch and T. truncatus Ehara.

Restriction Fragment Length Polymorphism Catalog for Molecular Identification of Japanese Tetranychus Spider Mites (Acari: Tetranychidae)

Abstract Species identification is a basic issue in biosecurity. Polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) is a useful molecular diagnostic tool for species identification. However, the lack of transferability of data has been a serious shortcoming of this method. A RFLP catalog, i.e., a graph of PCR-RFLP patterns expected from sequence data, was devised as a tool to facilitate PCR-RFLP data sharing among laboratories. Twelve species of Tetranychus spider mites have been recorded in Japan to date. In this study, we analyzed DNA sequences of the internal transcribed spacer (ITS) region in nuclear ribosomal DNA of 11 Tetranychus species. For the species identification using PCR-RFLP, we chose six candidates from 131 restriction endonucleases and developed an RFLP catalog of all known Japanese Tetranychus species except Tetranychus neocaledonicus André. The RFLP catalog revealed that most Tetranychus species had diagnostic restriction fragments. The RFLP catalog is transferable and simple molecular diagnostic tool, and it has the ability to add more species and newly found intraspecific variations. Therefore, we believe that the RFLP catalog will contribute to biosecurity as a practical diagnostic tool for species identification of spider mites.

Isolation, Characterization, Inheritance and linkage of Microsatellite Markers in Tetranychus kanzawai (Acari: Tetranychidae)

We isolated and characterized seven microsatellite markers in Tetranychus kanzawai (Acari: Tetranychidae). We also examined the conformity of the isolated markers to Mendelian laws and analyzed linkage among the microsatellite loci. All microsatellite markers fit expected 1:1 disomic segregation ratio and hence were inherited in a Mendelian manner. Significant pairwise linkage was detected in three pairs of microsatellite loci. These isolated microsatellite markers may become a powerful tool for the study of behavioral ecology, population genetics, and genome mapping of T. kanzawai.

Gene flow and spatio-temporal genetic variation among sympatric populations of Tetranychus kanzawai (Acari: Tetranychidae) occurring on different host plants, as estimated by microsatellite gene diversity.

We investigated spatio-temporal genetic variation in allele frequency and estimated gene flow among sympatric populations of Tetranychus kanzawai on different host plants by the use of microsatellite markers. In the analysis of spatial genetic variation, no isolation by distance was detected among the populations. Gene flow between populations on Hydrangea macrophylla and those on other host plants was relatively restricted, whereas the populations on Akebia quinata and Clerodendrum trichotomum were almost panmictic. Our study on temporal genetic variation showed (1) that population differentiation was slightly reduced during the period from April to May owing to frequent gene flow among populations; and (2) that population differentiation was greatly enhanced from May to October because of bottleneck effects. Genetic differentiation among T. kanzawai populations was caused by the effect of host plants rather than by the effect of geographic distance among populations, suggesting possibility of sympatric host race formation in this species.

DNA-Based Identification of Spider Mites: Molecular Evidence for Cryptic Species of the Genus Tetranychus (Acari: Tetranychidae)

ABSTRACT 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.

Phylogenetic analysis of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) based on the mitochondrial COI gene and the 18S and the 5' end of the 28S rRNA genes indicates that several genera are polyphyletic.

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.

Molecular-Based Identification and Phylogeny of Oligonychus Species (Acari: Tetranychidae)

ABSTRACT 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.

Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing

We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Newly amplified fragments from recombinant plasmids were mixed in various ratios to produce standard DNA template mixtures. After direct sequencing, the signal ratios between two nucleotides at each species-specific polymorphic site were calculated and shown against the corresponding expected ratios. Quadratic regression equations were used to estimate the phytoseiid mite species composition. Results showed that the phytoseiid mite species composition changed during the survey period and varied among study sites.

Mass fingerprint analysis of spider mites (Acari) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid discrimination

RATIONALE Discrimination of spider mite species is still performed using morphological information, although DNA and other biological approaches have been attempted for identification purposes. These techniques need much time, are expensive, and require specialist staff. As an alternative, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis is applied for rapid discrimination of spider mite species. METHODS Spider mites were analyzed using MALDI-TOFMS after extraction with 70% formic acid and acetonitrile. A single spider mite was also analyzed directly on double-sided carbon tape. A dendrogram was compiled from the MS data. RESULTS Evolutionarily close and morphologically similar spider mites, the Kanzawa (Tetranychus kanzawai) and the two-spotted (T. urticae) spider mites, as well as three other related species of spider mites, could be discriminated by mass fingerprints. Although female adults were mainly used in this report, male adults and nymphs showed almost the same mass fingerprints and were not considered to affect discrimination capability. A single spider mite on double-sided carbon tape was analyzed directly by MALDI-TOFMS. CONCLUSIONS Spider mites could be analyzed directly by MALDI-TOFMS, with evolutionarily and morphologically closely related spider mites showing different mass fingerprints, allowing for their identification.