PCR bias associated with conserved primer binding sites, used to determine genotype diversity within Citrus tristeza virus populations

Read, David Alan; Pietersen, G.

doi:10.1016/j.jviromet.2016.09.004

Cited by 7 publications

(1 citation statement)

References 37 publications

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“…In the presence of a coinfection, we would not expect to have sequenced such high quality SSU sequences due to the presence of two competing template strands. We hypothesize that our success may be the result of PCR bias (Chen et al 2011;Kurata et al 2004;Ogino and Wilson 2002;Read and Pietersen 2016 Figure 2 Phylogenetic relationships of the two microsporidian isolates presented in this publication (bolded) against other True Nosema and Nosema/Vairimorpha species based on concatenated SSU and ITS alignments and separated by clade. The relationsips are estimated using a Neighbor Joining model.…”

Section: Discussionmentioning

confidence: 99%

Using the SSU, ITS, and Ribosomal DNA Operon Arrangement to Characterize Two Microsporidia Infecting Bruce Spanworm, Operophtera bruceata (Lepidoptera: Geometridae)

Donahue

Broadley

Elkinton

et al. 2018

J Eukaryotic Microbiology

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Research pertaining to the two closely-related microsporidian genera Nosema and Vairimorpha is hindered by inconsistencies in species differentiation within and between the two clades. One proposal to better delimit these genera is to restructure the Nosema around a "True Nosema" clade, consisting of species that share a characteristic reversed ribosomal DNA operon arrangement and small subunit (SSU) ribosomal DNA sequences similar to that of the Nosema type species, N. bombycis. Using this framework, we assess two distinct microsporidia recovered from the forest insect Bruce spanworm (Operophtera bruceata) by sequencing their SSU and internal transcribed spacer regions. Phylogenetic analyses place one of our isolates within the proposed True Nosema clade close to N. furnacalis and place the other in the broader Nosema/Vairimorpha clade close to N. thomsoni. We found that 25% of Bruce spanworm cadavers collected over the four-year study period were infected with microsporidia, but no infections were detected in cadavers of the Bruce spanworm's invasive congener, the winter moth (O. brumata), collected over the same period. We comment on these findings as they relate to the population dynamics of the Bruce spanworm-winter moth system in this region, and more broadly, on the value of ribosomal DNA operon arrangement in Nosema systematics.

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Section: Discussionmentioning

confidence: 99%