Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies.

ABSTRACT: Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

SUBMITTER: Miyazaki K

PROVIDER: S-EPMC8601142 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete Genome Sequencing of Thermus thermophilus Strain HC11, Isolated from Mine Geyser in Japan.

Project description:Thermus thermophilus strain HC11 was isolated from Mine Geyser in Japan, where type strain HB8 was isolated 50?years ago. In this article, the complete genome sequence of HC11 is presented. HC11 shares the highest average nucleotide identity with HB8 among known T. thermophilus genomes (93.1%) with no genetic rearrangements.

| S-EPMC6763646 | biostudies-literature

Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan.

Project description:We isolated Thermus thermophilus strain HB5018 from Mine Hot Spring in Japan, where the type strain HB8 was isolated nearly half a century ago. The complete genome sequence of HB5018 showed 99.1% average nucleotide identity with HB8, suggesting strict species conservation in the habitat over the past 50 years.

| S-EPMC7953284 | biostudies-literature

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.

Project description:Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.

| S-EPMC6807382 | biostudies-literature

Genome Sequence of Thermus thermophilus ATCC 33923, a Thermostable Trehalose-Producing Strain.

Project description:Thermus thermophilus ATCC 33923 contains a thermostable enzyme that can efficiently catalyze the conversion of maltose into trehalose. Here we report a 2.15-Mb assembly of its genome sequence and other useful information, including the coding sequences (CDS) responsible for biological processes such as DNA replication, DNA repair, and RNA maturation.

| S-EPMC3735056 | biostudies-literature

Expression profile of TTHA1939-deficient Thermus thermophilus HB8 strain

Project description:We observed the expression profile of the total mRNA of the TTHA1939-deficient strain grown in a rich medium at 70°C for 800 min.

2010-10-15 | GSE21464 | GEO

Expression profile of TTHA1431-deficient Thermus thermophilus HB8 strain

Project description:In order to find function of TTHA1431 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA1431-deficient strain grown in a rich medium at 70°C for 360 min.

2010-10-15 | GSE21462 | GEO

Expression profile of TTHA0845-deficient Thermus thermophilus HB8 strain

Project description:In order to find function of TTHA0845 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0845-deficient strain grown in a rich medium at 70°C for 420 min.

2010-10-15 | GSE21461 | GEO

Expression profile of TTHA1634-deficient Thermus thermophilus HB8 strain

Project description:In order to find function of TTHA1634 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA1634-deficient strain grown in a rich medium at 70°C for 420, and 600 min.

2010-10-15 | GSE21460 | GEO

Expression profile of crp-deficient Thermus thermophilus HB8 strain

Project description:We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70 degC

2010-10-15 | GSE21459 | GEO

Expression profile of TTHA0252-deficient Thermus thermophilus HB8 strain

Project description:In order to find function of TTHA0252 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0252-deficient strain grown in a rich medium at 70°C for 360,540, and 680 min.

2010-10-15 | GSE21456 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data