Complete genome sequences of five Variovorax strains isolated from the Populus rhizosphere and endosphere

Beals, Delaney G.; Carrell, Alyssa A.; Rodriguez, Brisa; Alexander, William G.; Schadt, Christopher Warren; Hochanadel, Leah H.; Podar, Mircea; Pelletier, Dale A.

doi:10.1128/mra.00990-25

Complete genome sequences of five Variovorax strains isolated from the Populus rhizosphere and endosphere

Journal Article · Wed Jan 08 00:00:00 EST 2025 · Microbiology Resource Announcements

DOI:https://doi.org/10.1128/mra.00990-25· OSTI ID:3017012

^[1]; ^[1]; Rodriguez, Brisa ^[1]; ^[1]; ^[1]; ^[1]; ^[1]; ^[1]

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

We report the complete genome sequences of five Variovorax strains isolated from the roots of Populus species in greenhouse and field settings. Genome sizes range from 7.44 to 7.71 Mbp and encode 6,077–6,879 predicted protein-coding genes. These genome assemblies expand the known genomic catalog of Variovorax in plant-associated environments.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 3017012

Journal Information:: Microbiology Resource Announcements, Journal Name: Microbiology Resource Announcements Journal Issue: 1 Vol. 15; ISSN 2576-098X

Publisher:: SSPA - American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (17)

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11336	journal	August 2012
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07641-9	journal	November 2018
A single bacterial genus maintains root growth in a complex microbiome Finkel, Omri M.; Salas-González, Isai; Castrillo, Gabriel Nature, Vol. 587, Issue 7832 https://doi.org/10.1038/s41586-020-2778-7	journal	September 2020
Assembly of long, error-prone reads using repeat graphs Kolmogorov, Mikhail; Yuan, Jeffrey; Lin, Yu Nature Biotechnology, Vol. 37, Issue 5 https://doi.org/10.1038/s41587-019-0072-8	journal	April 2019
Time- and memory-efficient genome assembly with Raven Vaser, Robert; Šikić, Mile Nature Computational Science, Vol. 1, Issue 5 https://doi.org/10.1038/s43588-021-00073-4	journal	May 2021
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences Li, Heng Bioinformatics, Vol. 32, Issue 14 https://doi.org/10.1093/bioinformatics/btw152	journal	March 2016
Minimap2: pairwise alignment for nucleotide sequences Li, Heng Bioinformatics, Vol. 34, Issue 18 https://doi.org/10.1093/bioinformatics/bty191	journal	May 2018
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil Lerner, Harry; Öztürk, Başak; Dohrmann, Anja B. FEMS Microbiology Ecology, Vol. 97, Issue 5 https://doi.org/10.1093/femsec/fiab051	journal	March 2021
Cultivating the Bacterial Microbiota of Populus Roots Carper, Dana L.; Weston, David J.; Barde, Aditya mSystems, Vol. 6, Issue 3 https://doi.org/10.1128/mSystems.01306-20	journal	June 2021
Trycycler: consensus long-read assemblies for bacterial genomes Wick, Ryan R.; Judd, Louise M.; Cerdeira, Louise T. Genome Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s13059-021-02483-z	journal	September 2021
Benchmarking of long-read assemblers for prokaryote whole genome sequencing Wick, Ryan R.; Holt, Kathryn E. F1000Research, Vol. 8 https://doi.org/10.12688/f1000research.21782.4	journal	January 2019
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding Taye, Zelalem M.; Helgason, Bobbi L.; Bell, Jennifer K. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03007	journal	January 2020
New variochelins from soil-isolated Variovorax sp. H002 Haedar, Jabal Rahmat; Yoshimura, Aya; Wakimoto, Toshiyuki Beilstein Journal of Organic Chemistry, Vol. 20 https://doi.org/10.3762/bjoc.20.63	journal	April 2024

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