Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete genome sequence of Australian soil bacterium Rouxiella badensis DAR84756 resolved with Oxford Nanopore long-read and Illumina sequences.

ABSTRACT: The complete genome sequence of the bacterium Rouxiella badensis DAR84756, isolated from soil in Orange, NSW, Australia, was resolved using a combination of Nanopore long-read and Illumina short-read sequencing. The genome consists of a single, circular chromosome of 5,004,491 bp and a plasmid of 40,722 bp.

SUBMITTER: Paul S

PROVIDER: S-EPMC10793252 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete genome sequence of Australian soil bacterium Rouxiella badensis DAR84756 resolved with Oxford Nanopore long-read and Illumina sequences.

Paul Saina S Anderson Peter J PJ Maynard Gregg J GJ Dyall-Smith Michael M Kudinha Timothy T

Microbiology resource announcements 20231201 1

The complete genome sequence of the bacterium Rouxiella badensis DAR84756, isolated from soil in Orange, NSW, Australia, was resolved using a combination of Nanopore long-read and Illumina short-read sequencing. The genome consists of a single, circular chromosome of 5,004,491 bp and a plasmid of 40,722 bp. ...[more]

PMID: 38038462

Similar Datasets

Complete Genome Sequences of the Type Strains Rouxiella badensis DSM 100043 and R. chamberiensis DSM 28324, Resolved Using Nanopore Long-Read Sequencing.

Project description:The complete genome sequences of Rouxiella badensis DSM 100043T and Rouxiella chamberiensis DSM 28324T were determined using Oxford Nanopore long-read sequencing and the Flye assembler. The former contains a circular chromosome of 4,964,479 bp and a circular plasmid of 116,582 bp; the latter contains a circular chromosome of 4,639,296 bp.

| S-EPMC10353361 | biostudies-literature

Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA.

Project description:ObjectivesDevelopment of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.).Data descriptionLong-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.

| S-EPMC7913452 | biostudies-literature

Rouxiella badensis

Project description:Rouxiella badensis overview

| PRJNA668425 | ENA

Closed Genome Sequences of Clinical Neisseria gonorrhoeae Strains Obtained from Combined Oxford Nanopore and Illumina Sequencing.

Project description:Neisseria gonorrhoeae is the etiological agent of gonorrhea, the second most common notifiable disease in the United States. Here, we used a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequencing data to obtain closed genome sequences of nine clinical N. gonorrhoeae isolates.

| S-EPMC6395865 | biostudies-literature

Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes.

Project description:Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

| S-EPMC8059532 | biostudies-literature

Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot.

Project description:Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch's postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.

| S-EPMC9749400 | biostudies-literature

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies.

Project description:We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.

| S-EPMC7363880 | biostudies-literature

Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing.

Project description:Here, we describe the complete genome sequences of two Bordetella pertussis strains, FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species. Sequences were obtained using a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq 500 sequence data.

| S-EPMC6256476 | biostudies-literature

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-11327 | biostudies-arrayexpress

Recovery of small plasmid sequences via Oxford Nanopore sequencing.

Project description:Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of assessing their ability to recover small plasmid sequences. To do so, we sequenced DNA from seven plasmid-rich bacterial isolates in three different ways: ONT ligation, ONT rapid and Illumina. Using the Illumina read depths to approximate true plasmid abundance, we found that small plasmids (<20 kbp) were underrepresented in ONT ligation read sets (by a mean factor of ~4) but were not underrepresented in ONT rapid read sets. This effect correlated with plasmid size, with the smallest plasmids being the most underrepresented in ONT ligation read sets. We also found lower rates of chimaeric reads in the rapid read sets relative to ligation read sets. These results show that when small plasmid recovery is important, ONT rapid library preparations are preferable to ligation-based protocols.

| S-EPMC8549360 | biostudies-literature