Abundance and competition in PCR

Schlichter, Ursula; Bertioli, David J.

doi:10.1038/nbt1096-1202a

Cited by 4 publications

(4 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(three samples). Nonrecovery may have been because of amplicon competition during mixed-species PCR, whereby the DNA of some taxa is amplified more efficiently than that of others (Schlichter & Bertioli, 1996). In order to have directly comparable MOTU richness estimates above-and belowground, we omitted these species from the analysis, following Hiiesalu et al (2012).…”

Section: Discussionmentioning

confidence: 99%

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

et al. 2014

View full text Add to dashboard Cite

SummaryAlthough experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass.We examined relationships among AMF richness, above-and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes.In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below-than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass.Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.

show abstract

Section: Discussionmentioning

confidence: 99%

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

et al. 2014

View full text Add to dashboard Cite

show abstract

“…However, two species added to these samples were not detected by 454 sequencing, even though they both amplified well in single species samples (I. Hiiesalu, personal communication). Non‐recovery may have been because of competition during mixed‐species PCR, whereby the DNA of some taxa is amplified more efficiently than that of others (Schlichter & Bertioli 1996). This mechanism may also have been responsible for the fact that six species in the field that were observed to be rooted in the sampled plots were not detected using 454 sequencing.…”

Section: Discussionmentioning

confidence: 99%

Plant species richness belowground: higher richness and new patterns revealed by next‐generation sequencing

et al. 2011

View full text Add to dashboard Cite

Variation in plant species richness has been described using only aboveground vegetation. The species richness of roots and rhizomes has never been compared with aboveground richness in natural plant communities. We made direct comparisons of grassland plant richness in identical volumes (0.1 × 0.1 × 0.1 m) above and below the soil surface, using conventional species identification to measure aboveground richness and 454 sequencing of the chloroplast trnL(UAA) intron to measure belowground richness. We described above- and belowground richness at multiple spatial scales (from a neighbourhood scale of centimetres to a community scale of hundreds of metres), and related variation in richness to soil fertility. Tests using reference material indicated that 454 sequencing captured patterns of species composition and abundance with acceptable accuracy. At neighbourhood scales, belowground richness was up to two times greater than aboveground richness. The relationship between above- and belowground richness was significantly different from linear: beyond a certain level of belowground richness, aboveground richness did not increase further. Belowground richness also exceeded that of aboveground at the community scale, indicating that some species are temporarily dormant and absent aboveground. Similar to other grassland studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased significantly with fertility. These results indicate that conventional aboveground studies of plant richness may overlook many coexisting species, and that belowground richness becomes relatively more important in conditions where aboveground richness decreases. Measuring plant belowground richness can considerably alter perceptions of biodiversity and its responses to natural and anthropogenic factors.

show abstract

“…Although the reason why the coronavirus leaderless positive-strand genomic RNA is not observed during acute infection is unknown, we speculate that since there is highly active translation taking place and the factors involved in template switching are in active that the overall process leads to the predominant synthesis of leader-containing RNA. The overwhelming abundance of leader-containing genomic RNA may subsequently lead to undetectable leaderless genomic RNA due to the feature of PCR competition [56]. In contrast, replication may be limited during coronavirus persistence [37], and the leaderless RNA can gradually be detected (Fig.…”

Section: Discussionmentioning

confidence: 99%

A Leaderless Genome Identified during Persistent Bovine Coronavirus Infection Is Associated with Attenuation of Gene Expression

Liao

2013

PLoS ONE

View full text Add to dashboard Cite

The establishment of persistent viral infection is often associated with the selection of one or more mutant viruses. For example, it has been found that an intraleader open reading frame (ORF) in genomic and subgenomic mRNA (sgmRNA) molecules is selected during bovine coronavirus (BCoV) persistence which leads to translation attenuation of the downstream ORF. Here, we report the unexpected identification of leaderless genomes, in addition to leader-containing genomes, in a cell culture persistently infected with BCoV. The discovery was made by using a head-to-tail ligation method that examines genomic 5′-terminal sequences at different times postinfection. Functional analyses of the leaderless genomic RNA in a BCoV defective interfering (DI) RNA revealed that (1) the leaderless genome was able to serve as a template for the synthesis of negative-strand genome, although it cannot perform replicative positive-strand genomic RNA synthesis, and (2) the leaderless genome retained its function in translation and transcription, although the efficiency of these processes was impaired. Therefore, this previously unidentified leaderless genome is associated with the attenuation of genome expression. Whether the leaderless genome contributes to the establishment of persistent infection remains to be determined.

show abstract

Abundance and competition in PCR

Cited by 4 publications

References 4 publications

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

Plant species richness belowground: higher richness and new patterns revealed by next‐generation sequencing

A Leaderless Genome Identified during Persistent Bovine Coronavirus Infection Is Associated with Attenuation of Gene Expression

Contact Info

Product

Resources

About