scholarly journals In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4131 ◽  
Author(s):  
Christina L. Mogren ◽  
Jonathan Gary Lundgren
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
In Silico ◽  
Target Genes ◽  
Sequence Similarity ◽  
Phenotypic Effect ◽  
High Sequence Similarity ◽  
Dsrna Molecule ◽  
Dsrna Binding ◽  
Genomic Regions

Background Pesticidal RNAs that silence critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods Published studies that developed pesticidal double stranded RNAs (dsRNAs) were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of similarity with sequences in the honey bee genome were evaluated statistically. Results We identified 101 insecticidal RNAs sharing high sequence similarity with genomic regions in honey bees. The likelihood that off-target sequences were similar increased with the number of nucleotides in the dsRNA molecule. The similarities of non-target genes to the pesticidal RNA was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence similarity with pesticidal RNAs relative to other areas of the genome. Discussion Although sequence similarity does not itself guarantee a significant phenotypic effect in honey bees by the primary dsRNA, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.

scholarly journals In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)

2017 ◽  
Author(s):  
Christina L Mogren ◽  
Jonathan Gary Lundgren
Keyword(s):  
Honey Bee ◽  
Sequence Homology ◽  
Honey Bees ◽  
In Silico ◽  
Target Gene ◽  
Target Sequence ◽  
Phenotypic Effect ◽  
Dsrna Binding ◽  
High Sequence Homology ◽  
Genomic Regions

Background. Pesticidal RNAs silencing critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods. Published studies that developed pesticidal dsRNAs were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of sequence homology with the honey bee genome were evaluated statistically for each. Results. We identified 101 insecticidal dsRNAs sharing high sequence homology with genomic regions in honey bees. The likelihood of off-target sequence homology increased with the parent dsRNA length. Non-target gene binding was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence homology with pesticidal RNAs relative to other areas of the genome. Discussion. Although sequence homology does not itself guarantee a significant phenotypic effect in honey bees, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.

scholarly journals In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)

2017 ◽  
Author(s):  
Christina L Mogren ◽  
Jonathan Gary Lundgren
Keyword(s):  
Honey Bee ◽  
Sequence Homology ◽  
Honey Bees ◽  
In Silico ◽  
Target Gene ◽  
Target Sequence ◽  
Phenotypic Effect ◽  
Dsrna Binding ◽  
High Sequence Homology ◽  
Genomic Regions

Background. Pesticidal RNAs silencing critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods. Published studies that developed pesticidal dsRNAs were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of sequence homology with the honey bee genome were evaluated statistically for each. Results. We identified 101 insecticidal dsRNAs sharing high sequence homology with genomic regions in honey bees. The likelihood of off-target sequence homology increased with the parent dsRNA length. Non-target gene binding was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence homology with pesticidal RNAs relative to other areas of the genome. Discussion. Although sequence homology does not itself guarantee a significant phenotypic effect in honey bees, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.

scholarly journals Genetic diversity of the complementary sex-determiner (csd) gene in two closed breeding stocks of Varroa -resistant honey bees

Apidologie ◽  
2020 ◽  
Vol 51 (6) ◽  
pp. 1125-1132
Author(s):  
Lelania Bilodeau ◽  
Arian Avalos ◽  
Robert G. Danka
Keyword(s):  
Genetic Diversity ◽  
Honey Bee ◽  
Honey Bees ◽  
Sequence Similarity ◽  
Variable Region ◽  
Breeding Programs ◽  
Frequency Distributions ◽  
Low Genetic Diversity ◽  
Breeding Populations ◽  
Periodic Monitoring

AbstractHoney bee (Apis mellifera) breeding programs that use a closed mating system are particularly vulnerable to low genetic diversity. Inadequate diversity at the complementary sex-determiner (csd) locus is problematic and potentially catastrophic in honey bee populations because it causes low brood viability. In typical commercial populations, queens are open mated and csd diversity is fostered by high rates of introgression. In this study, we examine genetic diversity within the highly variable region (HVR) of csd in two stocks bred for resistance to Varroa destructor: Pol-line and Hilo, both of which use closed mating systems. We sampled 47 Pol-line colonies and 41 Hilo colonies and found 60 protein alleles that were condensed into 35 allele groupings by sequence similarity. We found that proportionately, HVR diversity levels were comparable with those in other closed breeding populations as well as open-mated populations of A. mellifera worldwide. Distinct patterns are observed among Pol-line and Hilo csd protein alleles in both the phylogeny and allele frequency distributions, suggesting early divergence of the two stocks. When compared with an African outgroup, both stocks shared alleles with the outgroup, suggesting ancestral lineages are present and not all diversity is due to new mutations. Periodic monitoring of csd diversity is recommended for closed breeding programs. The csd diversity data reported here are currently being used to make breeding decisions in these two mite-resistant populations of honey bees.

scholarly journals Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Leila Gharehdaghi ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Kang He ◽  
Taher Harkinezhad ◽  
Gholamhosein Tahmasbi ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Honey Bee ◽  
Honey Bees ◽  
Target Genes ◽  
Hippo Signaling ◽  
Plant Mirnas ◽  
Small Noncoding Rnas ◽  
Regulation Function ◽  
Regulation Functions ◽  
Insect Interactions

Abstract Background MicroRNA (miRNA) is a class of small noncoding RNAs, which targets on thousands of mRNA and thus plays important roles in many biological processes. It has been reported that miRNA has cross-species regulation functions between parasitoid-host, or plant-animal, etc. For example, several plant miRNAs enter into the honey bees and regulate gene expression. However, whether cross-species regulation function of miRNAs is a universal mechanism remains a debate question. Results We have evaluated transmission of miRNAs from sunflower and sedr plants into the midgut of honey bee using RNA-Seq analyses complemented with confirmation by RT-qPCR. The results showed that at least 11 plant miRNAs were found in the midgut of honey bee feeding by sunflower and sedr pollen. Among which, nine miRNAs, including miR-30d, miR-143, miR-148a, miR-21, let-7 g, miR-26a, miR-126, miR-27a, and miR-203, were shared between the sunflower- and sedr-fed honey bees, suggesting they might have essential roles in plant-insect interactions. Moreover, existence of these co-shared miRNAs presents a strong evidence to support the successful transmission of miRNAs into the midgut of the insect. In total, 121 honeybee mRNAs were predicted to be the target of these 11 plant-derived miRNAs. Interestingly, a sedr-derived miRNA, miR-206, targets on 53 honeybee genes. Kyoto Encyclopedia of Genes and Genome (KEGG) analyses showed that these target genes are significantly involved in hippo signaling pathway-fly, Wnt signaling pathway, and N-Glycan biosynthesis. Conclusions In summary, these results provide evidence of cross-species regulation function of miRNA between honeybee and flowering host plants, extending our understanding of the molecular interactions between plants and animals.

scholarly journals Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development

Vaccines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 408 ◽  
Author(s):  
Vipin Ranga ◽  
Erik Niemelä ◽  
Mahlet Z. Tamirat ◽  
John E. Eriksson ◽  
Tomi T. Airenne ◽  
...  
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Vaccine Development ◽  
Sequence Similarity ◽  
T Cell Response ◽  
Immune Defense ◽  
Structural Explanation ◽  
High Sequence Similarity ◽  
Human Major Histocompatibility Complex ◽  
Mhc Molecules

The emergence of the COVID-19 outbreak at the end of 2019, caused by the novel coronavirus SARS-CoV-2, has, to date, led to over 13.6 million infections and nearly 600,000 deaths. Consequently, there is an urgent need to better understand the molecular factors triggering immune defense against the virus and to develop countermeasures to hinder its spread. Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. The identified epitopes, each one of nine amino acids, have high sequence similarity to the equivalent epitopes of SARS-CoV virus, which are known to elicit an effective T cell response in vitro. Moreover, we give a structural explanation for the binding of SARS-CoV-2-epitopes to MHC molecules. Our data can help us to better understand the differences in outcomes of COVID-19 patients and may aid the development of vaccines against SARS-CoV-2 and possible future outbreaks of novel coronaviruses.

scholarly journals In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sakshi Piplani ◽  
Puneet Kumar Singh ◽  
David A. Winkler ◽  
Nikolai Petrovsky
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
Protein Docking ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
High Sequence Similarity ◽  
Virus Origin ◽  
Species Specific

AbstractThe devastating impact of the COVID-19 pandemic caused by SARS–coronavirus 2 (SARS-CoV-2) has raised important questions about its origins and the mechanism of its transfer to humans. A further question was whether companion or commercial animals could act as SARS-CoV-2 vectors, with early data suggesting susceptibility is species specific. To better understand SARS-CoV-2 species susceptibility, we undertook an in silico structural homology modelling, protein–protein docking, and molecular dynamics simulation study of SARS-CoV-2 spike protein’s ability to bind angiotensin converting enzyme 2 (ACE2) from relevant species. Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Interestingly, pangolin ACE2 showed the next highest binding affinity despite having a relatively low sequence homology, whereas the affinity of monkey ACE2 was much lower despite its high sequence similarity to hACE2. These differences highlight the power of a structural versus a sequence-based approach to cross-species analyses. ACE2 species in the upper half of the predicted affinity range (monkey, hamster, dog, ferret, cat) have been shown to be permissive to SARS-CoV-2 infection, supporting a correlation between binding affinity and infection susceptibility. These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission. This study highlights how in silico structural modelling methods can be used to rapidly generate information on novel viruses to help predict their behaviour and aid in countermeasure development.

scholarly journals Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants

2021 ◽  
Vol 22 (20) ◽  
pp. 11100
Author(s):  
Qi Xie ◽  
Xufeng Wang ◽  
Juan He ◽  
Ting Lan ◽  
Jiayu Zheng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Target Genes ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Family Members ◽  
Land Plants ◽  
Small Rna Sequencing ◽  
Evolutionary Divergence ◽  
High Sequence Similarity ◽  
Functional Differences

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.

scholarly journals Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

2019 ◽  
Author(s):  
Andrew C. Read ◽  
Matthew J. Moscou ◽  
Aleksey V. Zimin ◽  
Geo Pertea ◽  
Rachel S. Meyer ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Genome Assembly ◽  
Sequence Similarity ◽  
Rice Variety ◽  
Gene Families ◽  
Resistance Locus ◽  
High Sequence Similarity ◽  
Long Read ◽  
Genomic Regions

AbstractBackgroundLong-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes make up one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is rich in NLR genes.ResultsToward identification of the Xo1 gene, we combined Nanopore and Illumina reads to generate a high-quality genome assembly for Carolina Gold Select. We identified 529 full or partial NLR genes and discovered, relative to the reference, an expansion of NLR genes at the Xo1 locus. One NLR gene at Xo1 has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain and near-identical, tandem, C-terminal repeats. Across diverse Oryzeae, we identified two sub-clades of such NLR genes, varying in the presence of the zfBED domain and the number of repeats.ConclusionsWhole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci, providing context as well as content. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Further, the Carolina Gold Select genome assembly will facilitate identification and exploitation of other useful traits in this historically important rice variety.

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