Identification of astigmatid mites using the second internal transcribed spacer (ITS2) region and its application for phylogenetic study

Abstract

The second internal transcribed spacer (ITS2) of nuclear ribosomal DNA from 73 specimens of Astigmata was analyzed by PCR amplification and DNA sequencing. The length of the ITS2 region varied from 282 to 592 bp. The interspecific variation based on consensus sequences was more than 4.1%, while the intraspecific or intra-individual variation was from 0 to 5.7%. The variation between geographically separated populations (0-3.2%) was almost the same as the variation within strains. The sequences of the ITS2 region of Astigmata were concluded to be species-specific. The phylogenetic tree inferred from the ITS2 region supported Zachvatkin's morphological classification in the subfamily Rhizoglyphinae. The species-specific ITS2 sequence is useful for the species identification of astigmatid mites and for studying low-level phylogenetic relationships.

An Integrative Taxonomy of Molecular and Traditional Approaches for Identification of a Storage Mite, Aleuroglyphus Ovatus (Acari: Astigmata: Acaridae) in Malaysia

“…In the present study of A. ovatus, the length of the ITS2 sequences varied considerably (450 -490 bp). The results were consistent with studies reported by Noge et al (2005), in which a slightly higher intraspecific variation among the ITS2 sequences of A. ovatus was observed as compared to other astigmatid mites. Another reason was probably due to the ITS2 region of A. ovatus that was not homogenized completely within and/ or between individuals as been observed by Yang et al (2011).…”

“…The need for an expert taxonomist that requires skills and experience is a major drawback of this conventional method (Vargas et al, 2005). Moreover, several factors such as broken bodies, immature stages and closely morphological characters can also affect specific morphological identification (Colloff and Spieksma, 1992;Noge et al, 2005). The present study showed that the A. ovatus mite has its own morphological characteristics.…”

“…One of the most useful markers was the ITS2 rDNA gene where it is highly conserved in eukaryotes and, hence, is used to identify closely related species. The multiple copy number of this region has also been previously reported, which favors its amplification by polymerase chain reaction (PCR) from genomic DNA of dust mites (Noge et al, 2005;Wong et al, 2011;Thet-Em et al, 2012). In the present study of A. ovatus, the length of the ITS2 sequences varied considerably (450 -490 bp).…”

“…The primers will span a portion of the 5.8S rDNA, the full length ITS2 region and a part of the 28S rDNA of astigmatid mite (Noge et al, 2005). The amplification reaction contained 10 µl of DNA, 25 µl of 2X Taq PCR Master Mix, 2.5 µl of each primer (10 µM), and 10 µl nuclease free water in a total volume of 50 µl.…”

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

“…After these qualityfiltering steps, the 401 762 retained sequences were further clustered at 98.0% sequence similarity as implemented in CD-Hit 4.6.1 (Fu et al, 2012). Compared with the routinely used 97%, this threshold is a better proxy at species level in several groups of fungi , protists (Litaker et al, 2007) and animals (Noge et al, 2005). Of 16 437 clusters, 6823 (41.5%) were represented by a single sequence.…”