scholarly journals The impact of RNA secondary structure on read start locations on the Illumina sequencing platform

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0173023 ◽  
Author(s):  
Adam Price ◽  
Jaishree Garhyan ◽  
Cynthia Gibas
Keyword(s):  
Secondary Structure ◽  
Illumina Sequencing ◽  
Rna Secondary Structure ◽  
Sequencing Platform ◽  
The Impact ◽  
Illumina Sequencing Platform

scholarly journals Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data

2018 ◽  
Author(s):  
Shengcai Liu ◽  
Liyun Peng ◽  
Junfei Pan ◽  
Xiao Wang ◽  
Chunli Zhao ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Sequencing Data ◽  
Amaranthus Tricolor ◽  
Sequencing Platform ◽  
Transcriptome Database ◽  
Polymerase Chain ◽  
Illumina Sequencing Platform ◽  
Illumina Sequencing Data

Betalains are abundant in amaranth plants. Additionally, the betalain molecular structure and metabolic pathway differ from those of betanin in beet plants. To date, only a few studies have examined the regulatory roles of miRNAs in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 198 known and 41 novel miRNAs. Moreover, 216 miRNAs were distributed in 44 miRNA families, including miR156, miR159, miR160, miR166, miR172, miR319, miR167, miR396, and miR398. An analysis of all unigene sequences in an amaranth transcriptome database resulted in the detection of 493 target genes for the 239 screened miRNAs. The targets included SPL2, ARF18, ARF6, and NAC. A quantitative real-time polymerase chain reaction validation of 20 miRNAs and nine target genes revealed expression-level differences between the red and green sectors of amaranth leaves. This study involved the application of an Illumina sequencing platform to identify miRNAs regulating betalain metabolism in amaranth plants. The data presented herein may provide insights into the molecular mechanisms underlying the regulation of betalain biosynthesis in amaranth and other plant species.

scholarly journals Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting

2020 ◽  
Vol 21 (13) ◽  
pp. 4807 ◽  
Author(s):  
Ali Hosseini Rad SM ◽  
Alexander D. McLellan
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Vaccine Development ◽  
Viral Fitness ◽  
Host Cells ◽  
Splice Sites ◽  
Genomic Rna ◽  
Zoonotic Pathogen ◽  
The Impact

The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson–Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2-permissive host cells, we identified ten separate target sequences in the SARS-CoV-2 genome; three of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host is constrained by host miRNA defences. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineering conditional attenuation to vaccine development, as well as providing a better understanding of viral tropism and pathogenesis.

scholarly journals Comparative analysis of variation and selection in the HCV genome

2016 ◽  
Author(s):  
Juan Ángel Patiño-Galindo ◽  
Fernando González-Candelas
Keyword(s):  
T Cell ◽  
Secondary Structure ◽  
Positive Selection ◽  
Rna Secondary Structure ◽  
Purifying Selection ◽  
Risk Groups ◽  
Biological Properties ◽  
T Cell Epitopes ◽  
The Impact ◽  
Positively Selected Sites

AbstractGenotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure. Less than 10% of the genome was found to be under positive selection, and purifying selection was the main evolutionary force in both subtypes. We found differences in the number of positively selected sites between subtypes in several genes (Core, HVR2 inE2, P7, helicase inNS3andNS4a).Heterozygosity values in positively selected sites and the rate of non-synonymous substitutions were significantly higher in subtype HCV-1b. Logistic regression analyses revealed that similar selective forces act at the genome level in both subtypes: RNA secondary structure and CD4 T-cell epitopes are associated with conservation, while CD8 T-cell epitopes are associated with positive selection in both subtypes. These results indicate that similar selective constraints are acting along HCV-1a and HCV-1b genomes, despite some differences in the distribution of positively selected sites at independent genes.

scholarly journals Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting

2020 ◽  
Author(s):  
Ali Hosseini Rad SM ◽  
Alexander D. McLellan
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Viral Fitness ◽  
Host Cells ◽  
Splice Sites ◽  
Genomic Rna ◽  
Zoonotic Pathogen ◽  
Viral Attenuation ◽  
The Impact

AbstractThe SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation.

scholarly journals Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data

2018 ◽  
Author(s):  
Shengcai Liu ◽  
Liyun Peng ◽  
Junfei Pan ◽  
Xiao Wang ◽  
Chunli Zhao ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Sequencing Data ◽  
Amaranthus Tricolor ◽  
Sequencing Platform ◽  
Transcriptome Database ◽  
Polymerase Chain ◽  
Illumina Sequencing Platform ◽  
Illumina Sequencing Data

Betalains are abundant in amaranth plants. Additionally, the betalain molecular structure and metabolic pathway differ from those of betanin in beet plants. To date, only a few studies have examined the regulatory roles of miRNAs in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 198 known and 41 novel miRNAs. Moreover, 216 miRNAs were distributed in 44 miRNA families, including miR156, miR159, miR160, miR166, miR172, miR319, miR167, miR396, and miR398. An analysis of all unigene sequences in an amaranth transcriptome database resulted in the detection of 493 target genes for the 239 screened miRNAs. The targets included SPL2, ARF18, ARF6, and NAC. A quantitative real-time polymerase chain reaction validation of 20 miRNAs and nine target genes revealed expression-level differences between the red and green sectors of amaranth leaves. This study involved the application of an Illumina sequencing platform to identify miRNAs regulating betalain metabolism in amaranth plants. The data presented herein may provide insights into the molecular mechanisms underlying the regulation of betalain biosynthesis in amaranth and other plant species.

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