Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

KBase Narrative - Complete Genome Sequence of Acidovorax temperans strain LMJ

Dataset ·

We have isolated a new strain of Acidovorax temperans strain LMJ (hereafter called strain LMJ) from a contaminated Tris-Acetate-Phosphate (TAP) medium plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.SG0182 (a Chlamydomonas Library project (CLiP) strain). We sequenced the whole genome of the strain LMJ using the PacBio Sequel II technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. We present the whole genome sequence of this strain that offer insights into its coding and non-coding genes and its nearest taxonomic neighbors.

Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI ID:
2228677
Country of Publication:
United States
Language:
English

References (23)

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
GTDB-Tk v2: memory friendly classification with the genome taxonomy database journal October 2022
Identifying bacterial genes and endosymbiont DNA with Glimmer journal January 2007
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
Mash: fast genome and metagenome distance estimation using MinHash journal June 2016
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix journal April 2009
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data journal February 2016
Identification, variation and transcription of pneumococcal repeat sequences journal February 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies journal May 2012
BLAT---The BLAST-Like Alignment Tool journal March 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
Metagenome-assembled genome extraction and analysis from microbiomes using KBase journal November 2022
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
Translational recoding in archaea journal September 2012
FIGfams: yet another set of protein families journal September 2009
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life journal August 2018
Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source journal June 2020
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy journal September 2021
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010

Similar Records

KBase Narrative - Complete genome sequence of a novel Microbacterium sp. strain Clip185.
Dataset · Mon Nov 25 23:00:00 EST 2024 · OSTI ID:2479104

Complete genome sequence of Sphingobium yanoikuyae strain CC4533
Dataset · Mon Oct 06 00:00:00 EDT 2025 · OSTI ID:2997510

KBase Narrative - Methylobacterium fujisawaense Strain C14 Genomic Sequence
Dataset · Fri May 03 00:00:00 EDT 2024 · OSTI ID:2345706

Related Subjects