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KBase Narrative - Complete genome sequence of a novel Microbacterium sp. strain Clip185.

Dataset ·
 [1];  [2]
  1. University of West Georgia, School of Field Investigations and Experimental Sciences; Oak Ridge National Laboratory
  2. University of West Georgia, School of Computing, Analytics, and Modeling
We have isolated a new species of Microbacterium, an Actinobacterium. We have temporarily named this bacterium as Microbacterium sp. strain Clip185 (hereafter called strain Clip185) from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.RY0402.185141 (a Chlamydomonas Library project CLiP strain). We sequenced the whole genome of strain Clip185 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of this new Microbacterium species that offers 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:
2479104
Country of Publication:
United States
Language:
English

References (22)

GTDB-Tk v2: memory friendly classification with the genome taxonomy database journal October 2022
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
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
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
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
Translational recoding in archaea journal September 2012
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life journal August 2018
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
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
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
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data journal February 2016
BLAT---The BLAST-Like Alignment Tool journal March 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
FIGfams: yet another set of protein families journal September 2009

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