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140 results for “ribosomal genes”
Fig. 2 in Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family
Fig. 2. Metaphase plates of Mugil incilis after (a) C-banding and (b) AgNO -staining. Arrows indicate chromosome pair number 1.
Gene-guided discovery and ribosomal biosynthesis of anticancer moroidin peptides
<p>Moroidin is a bicyclic plant octapeptide with tryptophan side-chain crosslinks, originally isolated as a pain-causing agent from Australian stinging tree <em>Dendrocnide moroides</em>. Moroidin and its analog celogentin C, derived from <em>Celosia argentea</em>, are inhibitors of tubulin polymerization and, thus, lead structures for cancer therapy. However, low isolation yields from source plants and challenging organic synthesis hinder moroidin-based drug development. Here, we present biosynthesis as an alternative route to moroidin-type bicyclic peptides and report that they are ribosomally synthesized and posttranslationally modified peptides (RiPPs) derived from BURP-domain peptide cyclases in plants.</p> <p>This submission includes the 793 plant transcriptomes from the 1kp databases [1] of Table S2 which were assembled de novo by rnaSPAdes [2,3] and searched for moroidin peptide cyclases.</p> <ol> <li>Yan, Z., Carpenter, E.J., Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M. and Burleigh, J.G., 2014. Data access for the 1,000 Plants (1KP) project. <em>Gigascience</em>, <em>3</em>(1), pp.2047-217X.</li> <li>Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. and Pyshkin, A.V., 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. <em>Journal of computational biology</em>, <em>19</em>(5), pp.455-477.</li> <li>Bushmanova, E., Antipov, D., Lapidus, A. and Prjibelski, A.D., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. <em>GigaScience</em>, <em>8</em>(9), p.giz100.</li> </ol> <p> </p>
Fig. 1 in Phylogenetic position of the freshwater fish trypanosome, Trypanosoma ophiocephali (Kinetoplastida) inferred from the complete small subunit ribosomal RNA gene sequence
Fig. 1 The neighbor-joining tree of aquatic trypanosomes constructed from complete small subunit ribosomal RNA (SSrRNA) sequences indicating the systematic position of T. ophiocephali and phylogenetic relationships among the aquatic trypanosomes whose sequences are available. T. lewisi, T. theileri, and T. avium are taken as the outgroup. Bootstrap values are shown for the maximum parsimony/neighborjoining/Bayes analyses
Figure 6 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 6. Maximum likelihood (ML) tree of bufonid frogs based on nucleotide sequences of the mitochondrial 16S rRNA gene with Leptophryne borbonica as an outgroup. The bootstrap support (>50%) is indicated at nodes in the order of ML (500) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%). Specimens examined in this study are indicated by boldface type.
Figure 2 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 2. Maximum likelihood (ML) tree based on nucleotide sequences of the mitochondrial 16S rRNA gene from 88 haplotypes of frogs (Table 1), with Xenopus laevis as an outgroup. Bootstrap support (>50%) is indicated at nodes in the order of ML (1000) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%).
Figure 1 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 1. The nucleotide and deduced amino acid sequences of the P. xylostella RpS27a gene coding region. The deduced amino acid sequence is presented below the nucleotide sequence in a single letter. The nuclear localization signal sequence is shaded. The initial and termination codon are underlined. The stop codon is denoted with an asterisk.
Figure 5. Phylogenetic relationship between P. xylostella RpS27a in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 5. Phylogenetic relationship between P. xylostella RpS27a and some other species. Corresponding GenBank accession numbers are: M. sexta: ACY95367.1; P. dardanus: CAH04128.1; Bombyx mori: NP_001091826.1; P. polytes: BAM18943.1; P. xuthus: BAM17728.1; S. frugiperda: AAL62473.1; D. plexippus: EHJ77179.1; A. yamamai: BAD05031.1; P. xylostella: JX437934; T. rubida: AER92457.1; D. melanogaster: NP_476778.1; A. aegypti: AAS79344.1; C. quinquefasciatus: XP_001844485.1.
Figure 6 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 6. mRNA level of RpS27a in DS-strain and DR-strain of P. xylostella. All values are expressed as means ± SD. DS-strain: deltamethrin-susceptible strain; DR-strain: deltamethrinresistant strain. *P <0.01.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
Figure 1 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 1. Strict consensus of the four equally most parsimonious trees (L = 526; CI = 0.447; RI = 0.743) obtained from the phylogenetic analysis of sphaeriid mitochondrial 16S rDNA sequences. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene
<p>mTAGs is a tool for the taxonomic profiling of metagenomes. It detects sequencing reads belonging to the small subunit of the ribosomal RNA (SSU-rRNA) gene and annotates them through the alignment to full-length degenerate consensus SSU-rRNA reference sequences. The tool is capable of processing single-end and pair-end metagenomic reads, takes advantage of the information contained in any region of the SSU-rRNA gene and provides relative abundance profiles at multiple taxonomic ranks (Domain, Phylum, Class, Order, Family, Genus and OTUs defined at a 97% sequence identity cutoff).</p>
The nucleotides absent in genes of SARS-CoV-2 non-canonical subgenomic RNAs generate new Programmed -1 Ribosomal Frameshifting
<p>The data correspond to the article entitled: "dNTPs and adjuvant reagent solutions in 3’ RACE improve the characterization of noncanonical RNA SARS-CoV-2 genomes"</p> <p>R1. RACE 3’ Primer Blast Alignment. Contains BLAST alignments against the GenBank database using the consensus nucleotide sequence from the 3’ end of the SARS-CoV-2 genome and the polylinker. In addition, an illustration of the restriction enzyme pattern of the 3' RACE primer RV30AkCOVID19 and its synthesis by MALDI-TOF is included. The red box indicates the nucleotide sequence of the polylinker and the yellow box represents the 3' RACE primer along with the result of primer synthesis and purification.</p> <p>Graphic representation of the procedure for SARS-CoV-2 genome cDNA synthesis and design of the 3’ RACE RV30AkCOVID19 primer. The rectangle with vertical lines and the dots represents the 3’ RACE RV30AkCOVID19 primer and the polylinker, respectively, in the region complementary to the 3’ UTR end. The arrow represents the reverse transcriptase during complementary strand synthesis. The scissors represent RNases used in purification. The black spheres and magnets indicate the purification process using magnetism.</p> <p>R2. Reads and assembles SARS-CoV-2 genomes.</p> <p>The folder "1) Reads - Ion torrent" contains the reads obtained from sequencing via Ion Torrent technology and the reagents used in this study.</p> <p>The folder named "2) FastQC" contains the results of Ion Torrent sequencing. In the file name, the number indicates the sample, and the letters "RNA" indicate the sequencing according to the IonTorrent protocol. The cDNA synthesis procedures for this study correspond to the following nomenclature: dNTPs-R = dNTPs SARS-CoV-2 solution, DES-R = denaturation reagent, and COM PRO = commercial procedure.</p> <p>The folders named "3) IRMA" and "4) Bowtie2" contain the assemblies of the genomes.</p> <p>Regions and/or codons with loss of genomes 07dN120320 and 27sT122620.</p> <p>Mutations and amino acid substitutions of the SARS-CoV-2 genomes.</p> <p>In addition, an Excel document with the nucleotide ratios of each characterized genome is included from SARS-CoV-2.</p> <p>R3. BLAST alignment of assembled SARS-CoV-2 genomes. Contains two folders named "BLAST - IRMA" and "BLAST - Bowtie2," which contain plain text documents with the results of the BLAST alignment for the genomes obtained with each of the assemblies.</p> <p>R4. Pangolin v1.16 and Nextclade v2.9.1 lineages for SARS-CoV-2 genomes. Contains the folders "Pangolin and Nextclade (Bowtie2)" and "Pangolin and Nextclade (IRMA)." Each folder shows the data obtained with the Pangolin v1.16 and Nextclade v2.9.1 software for the classification of the genomes reported in this study, which were assembled with the IRMA and Bowtie2 software.</p> <p>R5. Reference genome alignment and assembled genomes. Contains the folders "1) IRMA genomes," "2) Bowtie2 genomes," and "3) Genomes 07dN120320 and 27St122620." The files show the sequences and alignments of the examined genomes (the file name indicates the analyzed genome) relative to the SARS-CoV-2 reference genome both in FASTA and Clustal W formats.</p> <p>R6. Programmed −1 Ribosomal Frameshifting Structure. The folder "1) Gibbs free energy 2D" contains a plain text document indicating the secondary structures of the open reading frame stimulation element in dot-bracket format. The folder "2) modeling Data Modeling 3D" contains the information for generating the structure of folder 1 in 3D.</p> <p>R7. SARS-CoV-2 Database.</p> <p>1) GISAID_sequences.zip contains a Zip file that contains a folder named GISAID, which in turn contains plain text documents with the genomes of each variant indicated in the filename of each document.</p> <p>2) The depuration of sequences_GISAID contains two subfolders. The first subfolder, named "1) SARS-CoV-2 complete genome" contains plain text documents with the genomes downloaded from GISAID without undetermined nucleotides. The file name of each document corresponds to the analyzed variant. The subfolder "2) SARS-CoV-2 eliminate genome" contains the sequences eliminated from subfolder 1 because they differed from the majority of the analyzed sequences.</p> <p>3) SARS-CoV-2 consensus variants. Contains plain text documents with consensus sequences for each variant, with frequency thresholds of 20 and 100 indicated in the file name of each document.</p> <p>4) SARS-CoV-2 alignment consensus variants. Contains two subfolders, with the number indicating the alignment frequency threshold. The "Alignment 20_" subfolder contains four documents named "with Ns," which correspond to fasta and Clustal formats with undetermined nucleotides, whereas the files named "without" do not have undetermined nucleotides. The "100_" folder has the same file pattern as the previous folder.</p> <p>5) SARS-CoV-2 codons alignment consensus variants and nc-sgRNA. Contains a document with the alignment of the genomes characterized in this study with the reference genome of SARS-CoV-2. A subfolder named “SARS-CoV-2 codons nc-sgRNA” shows each of the nc-sgRNA obtained in this study with the reference genome, and the file name corresponds to the nc-sgRNAs. The subfolder “SARS-CoV-2 Geneious Prime” contains 4 documents. Each document includes the graphical representation of the alignment of the nc-sgRNA obtained with each treatment for the synthesis of SARS-CoV-2 cDNA with respect to the reference genome. The following three documents indicated with the numbers 25, 50, and 100 correspond to the percentage of identity with respect to the number of annotations relative to the reference genome, which is indicated in the title of each document.</p> <p>6) Variant Alignment – Ns. Contains eight documents corresponding to the fasta and clustal formats with SARS-CoV-2 genomes obtained in this study from the reference genome and from genomes containing undetermined nucleotides of the Gamma, Lambda, Mu and Omicron variants.</p> <p>R8. Phylogeny SARS-CoV-2. Contains two subfolders with the results of the phylogenetic analyses conducted via the maximum likelihood method of the genomes characterized in this study compared to the variants. The subfolder named "Phylogeny with Ns" indicates the analysis of genomes containing undetermined nucleotides, whereas "Phylogeny without Ns" corresponds to the analysis of complete genomes.</p>
Supplementary material 1 from: Scacchetti P, Pansonato-Alves J, Utsunomia R, Oliveira C, Foresti F (2011) Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences. Comparative Cytogenetics 5(3): 223-235. https://doi.org/10.3897/compcytogen.v5i3.1375
Nexus file of aligned COI and COII nucleotide sequences.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
<p>With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage <i>in silico</i>. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the <i>Vitis</i> clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.</p>
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)
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FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
Supplementary material 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Full information and metadata about the genomic and metagenomic samples : Explanation note: Detailed information about metadata, DNA quality and genomic/metagenomic results of fruit-body and EcM root tip samples.
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OpenNeuro
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