The nuclear genome of the phytoseiid Metaseiulus occidentalis (Acari: Phytoseiidae) is among the smallest known in arthropods

Abstract

The genome size of the phytoseiid Metaseiulus (=Typhlodromus or Galendromus) occidentalis (Nesbitt) needs to be estimated before the whole nuclear genome can be sequenced. Two different procedures were used to estimate the genome size of M. occidentalis; (1) flow cytometry (Marescalchi et al. in Genome 33:789-793, 1990) and (2) quantitative real-time PCR (qRT-PCR) (Wilhelm et al. in Nucleic Acids Res 31:e56, 2003). Fluorescence intensity of propidium iodide-stained nuclei of M. occidentalis was measured by flow cytometry using females, males, and eggs. Only the eggs yielded peaks, which ranged in size from 35 to 160 Mb, with a tall peak of 140 Mb in 1-day-old eggs and 65 Mb in 2-day-old eggs, respectively. However, the peaks are broad and do not provide an accurate estimate. The qRT-PCR procedure required single-copy nuclear gene sequences from this phytoseiid. This was accomplished by designing degenerate primers, amplifying the Actin and EF1alpha sequences from M. occidentalis, and then designing M. occidentalis-specific primers that amplified a unique sequence. The standard qRT-PCR protocol was inefficient and amplification failed frequently, so we developed a high-fidelity qRT-PCR protocol, which utilizes a mix of two DNA polymerases (Taq and a proof-reading Tgo or ACCUZYME) to consistently amplify sequences. This allowed us to estimate the nuclear genome size of M. occidentalis as 88-90 +/- 5 Mb. When compared to other arthropod genomes, this appears to be very small.

The predatory miteMetaseiulusoccidentalis: mitey small and mitey large genomes

“…The products amplified from M. occidentalis were sequenced and were 100% identical to the known sequences. (40) When the genome size of M. occidentalis (88-90 Mb) is compared to other arthropods, it is slightly larger than that of its most important prey, the two-spotted spider mite Tetranychus urticae, which is reported to have a genome size of 75 Mb, (41)(42)(43) and is smaller than the genomes of all other studied arthropods (Fig. 5).…”

“…Estimates of the size were obtained using a quantitative real-time PCR (qRT-PCR) protocol and flow cytometry. (39)(40) The flow cytometry results indicated that the genome was significantly smaller (less than 100 Mb) than that of D. melanogaster, which was used as a control, but unambiguous estimates could not be obtained. However, the qRT-PCR protocol with two different genes yielded consistent results.…”

“…Only the complete sequence of a mariner transposable element (TE), (57) four Actin genes, and EF1-a have been obtained. (40) The lack of extensive nuclear gene sequence data limits our ability to design speciesspecific PCR primers that would allow us to identify this, and other morphologically similar, phytoseiid species. (58) Phytoseiids are relatively depauperate in morphological traits suitable for systematics and phylogenetic analysis and the lack of suitable nuclear gene sequences has led to taxonomic chaos.…”

Ancestral reconstruction of tick lineages

“…Apis mellifera, the total complement of the heme biosynthesis pathway could be obtained for the predatory parasitiform mite Metaseiulus occidentalis (hemA: 391339730; hemB: 391332178; hemC: 391347560; hemD: 391331139; hemE: 391332650; hemF: 391341014; hemG: 391332341; hemH: 391348503), that has the smallest chelicerate genome to date (Jeyaprakash and Hoy, 2009a). This indicates that the ability to synthesize heme existed in the ancestral parasitiform lineage.…”

Molecular discrimination of phytoseiids associated with the red palm mite Raoiella indica (Acari: Tenuipalpidae) from Mauritius and South Florida

“…The 12S rRNA gene has become a useful molecular marker for species resolution within the phytoseiids because it has a higher sequence divergence (9.5-45 %) than the ITS-2 region (1.2-23 %) between species (Navajas et al 1999;Hoy 2002, 2009b;Okassa et al 2009;Tixier et al 2010). The use of EF-Ia for phylogenetic resolution is still novel in the Phytoseiidae (Jeyaprakash and Hoy 2009a). It is considered to be a single-copy gene within the chelicerates (Brower and DeSalle 1994;Cruickshank 2002;Jeyaprakash and Hoy 2009a) and the faster-evolving intron sequences within this gene could provide species resolution (Cruickshank 2002).…”