a-loop-mediated-isothermal-amplification-lamp-assay-for-rapid

A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of <em>Bemisia tabaci</em>

The whitefly Bemisia tabaci (Gennadius) is an invasive pest of considerable importance, affecting the production of vegetable and ornamental crops in many ...

Agroscope

The mitochondrial genome is increasingly being used as a species diagnostic marker in insects. Typically, genomic DNA is PCR amplified and then analysed by restriction analyses or sequencing. This analysis system may cause some serious problems for molecular diagnosis. Besides the errors introduced by the PCR process, mtDNA sequence variation of amplified fragments may originate from mtDNA heteroplasmy or from nuclear integrations of mtDNA fragments, both of which have been shown to occur in insects. Here we document abundant variation in PCR-amplified sequences of the mitochondrial cytochrome oxidase I gene of Thrips tabaci. We confirm that the most common haplotype is of mitochondrial origin. Some of the observed mutations were introduced by the amplification process. However, the occurrence of some haplotypes at elevated frequencies indicates that within-individual variation of the respective fragment exists at low levels in T. tabaci. The frequencies of these sequences are too low to negatively affect mtDNA-based molecular diagnosis of T. tabaci. The possible origin of these variant haplotypes is discussed.

Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration?

Heteroplasmy in coding chloroplast DNA was only recently shown to occur and was so far not quantitatively assessed. We present a quantitative analysis of cpDNA heteroplasmy levels at a triazine-resistance determining site within and between individual Senecio vulgaris plants. Detectable levels of heteroplasmic haplotypes were observed in all tested plants. As expected, the levels of heteroplasmy vary greatly between plants. However, even within individual plants, the fraction of one haplotype may cover a range from below 1% to well over 90%. Our results suggest that heteroplasmy may be a common phenomenon in S. vulgaris. Possible consequences for molecular diagnostics of chloroplast encoded traits as well as evolutionary consequences of chloroplast heteroplasmy are discussed.

Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNA.

Here, we present the genome of a strain of Erwinia amylovora, the fire blight pathogen, with pathogenicity restricted to Rubus spp. Comparative genomics of ATCC BAA-2158 with E. amylovora strains from non-Rubus hosts identified significant genetic differences but support the inclusion of this strain within the species E. amylovora.

Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants.

Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5'end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.

Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation.

Article	Year
Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration? Hereditas\| PubMed ID: 15061785	2004
Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNA. Genetica\| PubMed ID: 15954496	2005
Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants. Journal of bacteriology\| PubMed ID: 21131493	2011
Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation. BMC evolutionary biology\| PubMed ID: 23718854	2013

Beatrice Frey

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