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opencc-by-4.0Nov 2024View details →

Oxford Nanopore Direct RNA Sequencing datasets for detecting rRNA modifications in the Brassica oleracea mitoribosome

Oxford Nanopore Direct RNA Sequencing (DRS) was applied for the detection of rRNA modifications in the Brassica oleracea mitoribosome. A comparison between native rRNA transcripts and in vitro transcribed (IVT) rRNA transcripts that were devoid of any modification indicated systematic base-calling errors and/or variations in current intensities that led to the prediction of the modified nucleotides (Begik et al., 2018). For Nanopore (DRS) library preparation, custom reverse transcription adapters (RTAs) containing Deeplexicon multiplexing barcodes (BC1, BC2 or BC3) were designed for sequence-specific ligation to the 3’-ends of B. oleracea mitochondrial rRNAs. Basecalling and demultiplexing of ONT direct RNA sequencing data were performed by Guppy and Deeplexicon, respectively. For the analysis and visualization of current intensities, a full description is available in the associated publication. The Eventalign_18S.R Rscript was used to make the nanopore 18S signal analysis The Eventalign_26S.R Rscript was used to make the nanopore 26S signal analysis The raw data for the scripts are in the following folders: - For 26S: 26S_Native.barcode01 and 26S_IVT.barcode03 - For 18S: 18S_Native.barcode01 and 18S_IVT.barcode02 These folders contain the read alignment files output from minimap2 (in .bam format) and the eventalign files generated by the f5c software (in tsv format). The FASTA folder contains the mitochondrial 18S and 26S rRNA gene reference sequence in fasta format

opencc-zeroDec 2021View details →

MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

<h1>Data sources</h1> This dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174). <h1>Sequencing data QC and metagenomic assembly</h1> First, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed. <h1>MAGs recovery</h1> MAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%). <h1>Non-redundant gene catalog</h1> Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives. <h1>MSPs recovery</h1> A raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer. <h1>MAGs and MSPs taxonomic annotation</h1> Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs. <h1>Construction of the phylogenetic tree</h1> 39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB38174 (cohort used in catalogue assembly) and PRJEB29033, PRJEB33338, PRJEB53667 (independent cohort not used in assembly).

opencc-zeroDec 2021View details →

MicroReset: characterization of the rabbit (Oryctolagus cuniculus) fecal metagenome and resistome by deep shotgun sequencing

<h1>Data source</h1> The dataset was generated from 30 rabbit fecal samples subjected to deep shotgun metagenomic sequencing. The sequencing data is available under the BioProject PRJEB50625. Metagenomic Assembly Raw sequencing reads were first pre-processed using fastp for adapter removal and quality trimming. Host-derived reads were filtered out by mapping to the rabbit reference genome (GCF_000001635.27) using Bowtie2 and removing mapped reads with Samtools. Each sample was individually assembled using metaSPAdes. Contigs shorter than 1,500 bp were excluded from downstream analysis. <h1>MAG Recovery</h1> Reads from each sample were mapped to all 30 assemblies (30×30 mappings) using Bowtie2. The resulting alignments were sorted and indexed with Samtools. Contig coverage across all samples was computed using `jgi_summarize_bam_contig_depths`. Binning was performed with MetaBAT 2 and SemiBin v1.3. MAG quality was assessed with CheckM. Only high-quality MAGs (≥70% completeness, ≤5% contamination, N50 ≥ 8 kb) were retained. Non-Redundant Gene Catalog Gene prediction was carried out using Prodigal on all contigs from the current study (with `-m -p meta`). Genes shorter than 90 bp or lacking start/stop codons were discarded. The remaining genes from both sources were pooled and clustered using CD-HIT-EST (parameters: `-c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0`). The longest contigs were used to select representative genes. <h1>MSP Recovery</h1> Shotgun reads from the 30 samples were aligned to the non-redundant gene catalog using the Meteor suite, generating a gene abundance matrix (5.7 million genes × 30 samples). Co-abundant genes were grouped into 1,053 Metagenomic Species Pan-genomes (MSPs) using MSPminer. <h1>Taxonomic Annotation of MSPs</h1> MAGs representing each species were taxonomically annotated using GTDB-Tk with GTDB release r214. The resulting taxonomy was propagated to the corresponding MSPs. <h1>Phylogenetic Tree Construction</h1> A set of 39 universal phylogenetic marker genes was extracted from the 1,053 MSPs (or their corresponding MAGs, when available) using fetchMGs. Each marker was independently aligned using MUSCLE, and the alignments were concatenated and trimmed using trimAl (parameter: `-automated1`). A maximum-likelihood phylogenetic tree was constructed with FastTreeMP (parameters: `-gamma -pseudo -spr -mlacc 3 -slownni`).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB50625 (cohort used in catalogue assembly).

Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids (Source Data)

Source data for Chemical Science paper "Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids" DOI: 10.1039/D3SC02761A

Supplementary Materials for: Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China

Supplementary Materials forDiscovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, ChinaAdrian Jones, Daoyu Zhang, Steven E. Massey,  Yuri Deigin, Louis R. Nemzer, Steven C. Quay

Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data

Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.Image data consists of:<ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul>Gene and cluster marker data is collected in the markers.h5ad file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>.

Genome Sequence Assembly of Coffea arabica variety Geisha (UCDv1.0)

Genome Sequence Assembly of Coffea arabica variety Geisha (UCDv1.0)

opencc-zeroOct 2023View details →

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Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees

Plants originally identified as Aphyllon ludovicianum that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative A. multiflorum, or any other species of Aphyllon. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study and georeferenced color photographs, we propose the new binomials Aphyllon spectabile for the plants from Nuevo Leon and Aphyllon gypsophilum for the plants from Coahuila, Mexico. This increases the taxonomic diversity of Aphyllon to 27 species plus ten additional subspecies. Gymnosperma glutinosum and two species of Xanthisma were reported for the first time as a host species for the genus Aphyllon. We also provide an updated key to Aphyllon in Mexico.

opencc-by-4.0Nov 2023View details →

High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences

Background: Xanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.Results: In this study, we produced high-quality, complete genome sequences of four strains of Xtg, complementing the recently obtained complete genome sequence of the Xtg pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found in Xtg and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes. Conclusion: These results suggest a high adaptability of Xtg, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific to Xtg were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of Xtg.

opennotspecifiedDec 2007View details →

FIGURES 23–31. Stenelmis puberula larva, 23 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences

FIGURES 23–31. Stenelmis puberula larva, 23) protergum, lateral depression with rimmed setiferous pits; 24) protergum, posterior angle; 25) long tergal seta; 26) meso- and metasternum, ventral view; 27) right fore-leg, ventral view; 28) left fore-leg, dorsal view; 29) fore-leg, detail of femur; 30) fore-leg, detail of tibia; 31) fore-leg, detail of tarsungulus.

opennotspecifiedDec 2007View details →

FIGURES 12–22. Stenelmis puberula larva, 12 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences

FIGURES 12–22. Stenelmis puberula larva, 12) left mandible, ventral view; 13) right mandible, ventral view; 14) left maxilla, ventral view; 15) same, detail of prebasal tufted scales; 16) left maxilla, detail of lateral seta; 17) right maxilla – galea, lacinia, palpus, ventral view; 18) mouth parts, ventral view; 19) labium, ventral view; 20) labial palpus, ventral view; 21) same, detail of apical sensory field; 22) labium, dorsal view.

opennotspecifiedDec 2007View details →

FIGURES 32–42. Stenelmis puberula larva, 32 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences

FIGURES 32–42. Stenelmis puberula larva, 32) right mid-leg, dorsal view; 33) left hind-leg, dorsal view; 34) mid-leg, detail of tibia; 35) hind-leg, detail of femur-tibia articulation; 36) detail of abdominal forked scales; 37) detail of abdominal tergum, lateral view; 38) venter of abdominal segments; 39) abdominal tergites, dorsal view; 40) abdominal segment 9, dorsal view; 41) abdominal segment 9, lateral view; 42) abdominal operculum, hooks and anal gills.

FIGURE 17 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 17. Black adult male Bungarus candidus (UK B15) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Like the type specimen of Bungarus javanicus, it has a yellow ventral colouration and yellow spots on the vertebrals. Note unpigmented internasals and 5th and 6th supralabials of the right head side. Photo by Ulrich Kuch.

FIGURE 16 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 16. Close-up of a black adult male Bungarus candidus (UK BP4) from the area of Purwokerto, Central Java, Indonesia. Photo by Ulrich Kuch.

FIGURE 15 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 15. The most frequently encountered colour morph of "black" Bungarus candidus on Java represented by an adult male (UK BX3) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Photo by Ulrich Kuch.

FIGURE 13 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 13. Adult female Bungarus candidus (UK B34) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the anterior body and mosaic-like dark stippling on the posterior body and tail. Photo by Ulrich Kuch.

FIGURE 11 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 11. Adult male Bungarus candidus (UK B38) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the posterior half of the body. Photo by Ulrich Kuch.

FIGURE 14 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 14. Adult male Bungarus candidus (UK B35) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced bands on the posterior body and heavy pigmentation of all light interspaces and ventrolateral areas (opaque colouration is due to imminent shedding). Photo by Ulrich Kuch.

FIGURE 10 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 10. Regularly black-and-white banded juvenile Bungarus candidus from Desa Songgon, about 20 km SW of Banyuwangi, East Java, Indonesia. Note the characteristic light head pattern of juvenile specimens. Photo by Andrea Glässer-Trobisch and Dietmar Trobisch.

FIGURE 9 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology

FIGURE 9. Black juvenile Bungarus candidus (ZMB 57702) from Banjar Berawa, Desa Canggu, Denpasar, Bali, Indonesia. Photo by Frank Tillack.