clonal population
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mBio ◽  
2021 ◽  
Vol 12 (6) ◽  
Author(s):  
Setsu Kato ◽  
Kenta Suzuki ◽  
Taiki Kenjo ◽  
Junya Kato ◽  
Yoshiteru Aoi ◽  
...  

Cells display various behaviors even though they originate from a clonal population. Such diversity is also observed in cell survival in the stationary phase of Saccharomyces cerevisiae .


2021 ◽  
Vol 102 (11) ◽  
Author(s):  
Emeline Ricciuti ◽  
Nathalie Laboureau ◽  
Guy Noumbissié ◽  
Matthieu Chabannes ◽  
Natalia Sukhikh ◽  
...  

The main edible and cultivated banana varieties are intra- and interspecific hybrids of the two main Musa species, Musa acuminata and Musa balbisiana, having diploid genomes denoted A and B, respectively. The B genome naturally hosts sequences of banana streak virus (BSV) named endogenous BSV (eBSV). Upon stress, eBSVs are identified as the origin of BSV infection for at least three BSV species, causing banana streak disease. For each of the three species, BSV and eBSV share >99.9 % sequence identity, complicating PCR-based diagnosis of viral infection in the B genome-containing bananas. Here, we designed a quantitative PCR-based method to only quantify episomal BSV particles produced, overcoming the limitation of eBSV also being detected by qPCR by using it as a ‘calibrator’. However, our results revealed unexpected variation of eBSV amplification in calibrator plants composed of a clonal population of 53 replicating virus-free banana hybrids with the same AAB genotype. Our in-depth molecular analyses suggest that this calibrator variation is due to the variable abundance of non-encapsidated extrachromosomal viral DNA, likely produced via the transcription of eBSVs, followed by occasional reverse transcription. We also present evidence that accumulation of viral transcripts in AAB plants is downregulated both at post-transcriptional and transcriptional levels by an RNA interference mechanism that keeps the plants free of virus infection. Finally, we recommend that such eBSV amplification variation be taken into account to establish a quantitative viral diagnostic for banana plants with the B genome.


2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Arnar K. S. Sandholt ◽  
Aleksija Neimanis ◽  
Anna Roos ◽  
Jenny Eriksson ◽  
Robert Söderlund

AbstractA type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.


2021 ◽  
Vol 118 (43) ◽  
pp. e2019060118
Author(s):  
Lufeng Dan ◽  
Yuze Li ◽  
Shuhua Chen ◽  
Jingbo Liu ◽  
Yu Wang ◽  
...  

Most genetic changes have negligible reversion rates. As most mutations that confer resistance to an adverse condition (e.g., drug treatment) also confer a growth defect in its absence, it is challenging for cells to genetically adapt to transient environmental changes. Here, we identify a set of rapidly reversible drug-resistance mutations in Schizosaccharomyces pombe that are caused by microhomology-mediated tandem duplication (MTD) and reversion back to the wild-type sequence. Using 10,000× coverage whole-genome sequencing, we identify nearly 6,000 subclonal MTDs in a single clonal population and determine, using machine learning, how MTD frequency is encoded in the genome. We find that sequences with the highest-predicted MTD rates tend to generate insertions that maintain the correct reading frame, suggesting that MTD formation has shaped the evolution of coding sequences. Our study reveals a common mechanism of reversible genetic variation that is beneficial for adaptation to environmental fluctuations and facilitates evolutionary divergence.


2021 ◽  
Author(s):  
Søren Vedel ◽  
Andrej Košmrlj ◽  
Harry Nunns ◽  
Ala Trusina

Abstract By diversifying, cells in a clonal population can together overcome the limits of individuals. Diversity in single-cell growth rates allows the population to survive environmental stresses, such as antibiotics, and grow faster than undiversified population. These functional cell-cell variations can arise stochastically, from noise in biochemical reactions, or deterministically, by asymmetrically distributing damaged components. While each of the mechanism is well understood, the effect of the combined mechanisms is unclear. To evaluate the contribution of the deterministic component we mapped the growing population to the Ising model. Model results, confirmed by simulations and experimental data, show that cell-cell variations increase near-linearly with stress. As a consequence, we predict that the entropic gain — the gain in population doubling time compared to an “average” cell — is primarily stochastic at low stress but crosses over to deterministic at higher stresses. Furthermore, we find that while the deterministic component minimizes population damage, stochastic variations antagonize this effect. Together our results may help identifying stress-tolerant pathogenic cells and thus inspire novel antibiotic strategies.


2021 ◽  
Vol 6 ◽  
pp. 225
Author(s):  
Eerik Aunin ◽  
Ulrike Böhme ◽  
Damer Blake ◽  
Alexander Dove ◽  
Michelle Smith ◽  
...  

We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.


2021 ◽  
Vol 9 (9) ◽  
pp. 1883
Author(s):  
Paloma Acebo ◽  
Cristina Herranz ◽  
Lucas Bernal Espenberger ◽  
Alicia Gómez-Sanz ◽  
María Carmen Terrón ◽  
...  

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide, and about 30% of the pneumococcal clinical isolates show type I pili-like structures. These long proteinaceous polymers extending from the bacterial surface are encoded by pilus islet 1 and play major roles in adhesion and host colonization. Pili expression is bistable and is controlled by the transcriptional activator RlrA. In this work, we demonstrate that the previously identified small noncoding RNA srn135 also participates in pilus regulation. Our findings show that srn135 is generated upon processing of the 5′-UTR region of rrgA messenger and its deletion prevents the synthesis of RrgA, the main pili adhesin. Moreover, overexpression of srn135 increases the expression of all pili genes and rises the percentage of piliated bacteria within a clonal population. This regulation is mediated by the stabilization of rlrA mRNA since higher levels of srn135 increase its half-life to 165%. Our findings suggest that srn135 has a dual role in pilus expression acting both in cis- (on the RrgA levels) and in trans- (modulating the levels of RlrA) and contributes to the delicate balance between pili expressing and non-expressing bacteria.


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