Abstract:We examined the epiphytic microbiome of cereal grain using the universal barcode chaperonin-60 (cpn60). Microbial community profiling of seed washes containing DNA extracts prepared from field-grown cereal grain detected sequences from a fungus identified only to Class Sordariomycetes. To identify the fungal sequence and to improve the reference database, we determined cpn60 sequences from field-collected and reference strains of the ergot fungus, Claviceps purpurea. These data allowed us to identify this fung… Show more
“…6 , Supplementary Information 12 ). A control experiment with fungi-specific primers confirmed absence of gDNA of Epichloë and Claviceps species, especially the rye ergot fungus, C. purpurea , in the retail products 24 , 29 . Figure 6 PCR-based detection of Lp FTRL-related gene from retail products.…”
Section: Resultsmentioning
confidence: 89%
“…The close physical contacts between the host plants and symbiotic and/or pathogenic fungi could have facilitated the relatively frequent transfer events 21 . As both Epichloë and Claviceps species infect plant reproductive tissues 24 , 29 , the presence close to germ cells might have been an important factor of the multiple HGT events 31 .…”
Section: Discussionmentioning
confidence: 99%
“…The β-1,6-glucanase-like gene ( Lp BGNL) of perennial ryegrass ( Lolium perenne L.; Poeae tribe, Loliinae sub-tribes) was the first documented candidate for an ancestral nuclear gene transfer event from non-plant species into the angiosperm lineage. A high sequence similarity (90%) to the corresponding gene of Epichloë species inferred that the gene was transferred from an ancestral species of the Epichloë taxon, which composes a sister group to the ergot fungi (the genus Claviceps ) 24 . As asexual Epichloë species may establish symbiotic relationships between the Loliinae and Dactylidinae species, close physical contact may have facilitated the HGT.…”
Evidence for ancestral gene transfer between Epichloë fungal endophyte ancestors and their host grass species is described. From genomes of cool-season grasses (the Poeae tribe), two Epichloë-originated genes were identified through DNA sequence similarity analysis. The two genes showed 96% and 85% DNA sequence identities between the corresponding Epichloë genes. One of the genes was specific to the Loliinae sub-tribe. The other gene was more widely conserved in the Poeae and Triticeae tribes, including wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). The genes were independently transferred during the last 39 million years. The transferred genes were expressed in plant tissues, presumably retaining molecular functions. Multiple gene transfer events between the specific plant and fungal lineages are unique. A range of cereal crops is included in the Poeae and Triticeae tribes, and the Loliinae sub-tribe is consisted of economically important pasture and forage crops. Identification and characterisation of the 'natural' adaptation transgenes in the genomes of cereals, and pasture and forage grasses, that worldwide underpin the production of major foods, such as bread, meat, and milk, may change the ‘unnatural’ perception status of transgenic and gene-edited plants.
“…6 , Supplementary Information 12 ). A control experiment with fungi-specific primers confirmed absence of gDNA of Epichloë and Claviceps species, especially the rye ergot fungus, C. purpurea , in the retail products 24 , 29 . Figure 6 PCR-based detection of Lp FTRL-related gene from retail products.…”
Section: Resultsmentioning
confidence: 89%
“…The close physical contacts between the host plants and symbiotic and/or pathogenic fungi could have facilitated the relatively frequent transfer events 21 . As both Epichloë and Claviceps species infect plant reproductive tissues 24 , 29 , the presence close to germ cells might have been an important factor of the multiple HGT events 31 .…”
Section: Discussionmentioning
confidence: 99%
“…The β-1,6-glucanase-like gene ( Lp BGNL) of perennial ryegrass ( Lolium perenne L.; Poeae tribe, Loliinae sub-tribes) was the first documented candidate for an ancestral nuclear gene transfer event from non-plant species into the angiosperm lineage. A high sequence similarity (90%) to the corresponding gene of Epichloë species inferred that the gene was transferred from an ancestral species of the Epichloë taxon, which composes a sister group to the ergot fungi (the genus Claviceps ) 24 . As asexual Epichloë species may establish symbiotic relationships between the Loliinae and Dactylidinae species, close physical contact may have facilitated the HGT.…”
Evidence for ancestral gene transfer between Epichloë fungal endophyte ancestors and their host grass species is described. From genomes of cool-season grasses (the Poeae tribe), two Epichloë-originated genes were identified through DNA sequence similarity analysis. The two genes showed 96% and 85% DNA sequence identities between the corresponding Epichloë genes. One of the genes was specific to the Loliinae sub-tribe. The other gene was more widely conserved in the Poeae and Triticeae tribes, including wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). The genes were independently transferred during the last 39 million years. The transferred genes were expressed in plant tissues, presumably retaining molecular functions. Multiple gene transfer events between the specific plant and fungal lineages are unique. A range of cereal crops is included in the Poeae and Triticeae tribes, and the Loliinae sub-tribe is consisted of economically important pasture and forage crops. Identification and characterisation of the 'natural' adaptation transgenes in the genomes of cereals, and pasture and forage grasses, that worldwide underpin the production of major foods, such as bread, meat, and milk, may change the ‘unnatural’ perception status of transgenic and gene-edited plants.
“…A PCR assay was performed using the Luna Universal qPCR Master Mix kit [New England BioLabs (NEB)] on the CFX Connect Real-Time PCR Detection System (BioRad). As the Epichloë genus and its next close genus, Claviceps, include species infectious to grass plants of the Pooideae subfamily, absence of those fungal species in plant genomic DNA (gDNA) samples was confirmed with Epichloë and Claviceps-specific primers [10,14,15].…”
Recent studies have revealed presence of fungus-originated genes in genomes of cool-season grasses, suggesting occurrence of multiple ancestral gene transfer events between the two distant lineages. The current article describes identification of glucanase-like and monooxygenase-like genes from creeping bent grass, as lateral gene transfer candidates. An in silico analysis suggested presence of the glucanase-like gene in Agrostis, Deyeuxia, and Polypogon genera, but not in other species belonging to the clade 1 of the Poeae tribe. Similarly, the monooxygenase-like gene was confined to Agrostis and Deyeuxia genera. A consistent result was obtained from PCR-based screening. The glucanase-like gene was revealed to be ubiquitously expressed in young seedlings of creeping bent grass. Although expression of the monooxygenase-like gene was suggested in plant tissues, the levels were considerably lower than those of the glucanase-like gene. A phylogenetic analysis revealed close relationships of the two genes between the corresponding genes in fungal endophyte species of the Epichloë genus, suggesting that the genes originated from the Epichloë lineage.
“…The ability to be more tolerant to inhibitor(s) is another major advantage of ddPCR, as use of a digital positive or negative assay result rather than number of cycles to achieve a given threshold of reaction product signal accumulation removes the reliance on PCR amplification efficiency to reduce error rates. Due to these advantages, ddPCR has seen increased utility in fields that involve nucleic acid detection and quantification, which include but are not limited to rare allele/mutation detection [1][2][3][4][5], detection of pathogens including viruses [6][7][8], gene expression, miRNA analysis and copy number variation (CNV) determination [9][10][11], as well as absolute quantification of nucleic acid reference reagents, standards and NGS libraries [12].…”
Accurate and sensitive quantification of rebound competent HIV that persists despite combination antiretroviral treatment (cART), including in latently infected cells (i.e., viral reservoir), is critical for evaluating cure strategies for decreasing or eliminating this reservoir. Simian immunodeficiency virus (SIV)-infected Rhesus macaques are an important non-human primate (NHP) system for studying potential cure strategies as they model many key aspects of human HIV-infection including the persistence of a latent viral reservoir in resting memory CD4+ T cells in animals receiving prolonged cART. In this report, we describe the design and testing of a sensitive SIV droplet digital PCR (ddPCR) assay through exploring the combination and optimization of different probe systems (including single, double quencher probes and minor groove binder (MGB) probes) and reaction conditions to eliminate background signal(s), ensure distinct target signal cluster separation from non-target signals, and enable detection and quantification of low level authentic target signals. Similar reaction conditions and assay validation procedures can be explored for potential development of additional assays for other applications that require sensitive detection of low-level targets in a large background of nucleic acid input derived from cell or tissue sources.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
