Open access
Announcement
19 March 2020

Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots

ABSTRACT

Larkinella sp. strain BK230, a heterotrophic bacterium of the phylum Bacteroidetes, was isolated from the roots of a field-grown eastern cottonwood tree (Populus deltoides) located in Georgia. The draft 7.27-Mb genome has a G+C content of 53.4% and contains 6,026 coding sequences, including 41 tRNA genes.

ANNOUNCEMENT

The genus Larkinella, a member of the Cytophagaceae family within the bacterial phylum Bacteroidetes, encompasses 9 named species (http://www.bacterio.net/larkinella.html), with only 5 being represented by genome sequence data. Here, we report the draft genome sequence of Larkinella sp. strain BK230, which was isolated from a Populus deltoides root sample collected from a field site in Georgia. This genomic information will enable comparative studies of tree root endophytes and the mechanisms of microbe-plant associations. Fine roots (<0.2 mm in diameter) were harvested from Populus deltoides WV94, growing on a nursery site in Bellville, Georgia, in September 2017. Washed root tissue was ground, and dilutions were plated on Reasoner’s 2A (R2A) agar and incubated for 7 days at 25°C. Pale-pink colonies that developed were isolated and subsequently identified by small-subunit rRNA gene amplicon sequencing (1). Based on 1,373 bases of 16S sequences from strain BK230 and a number of reference strains, a ClustalW v2.1 alignment and a neighbor-joining phylogenetic tree generated using Geneious v11 (2) indicated that the closest relatives of strain BK230 were Larkinella insperata and Larkinella arboricola, with 96.2% and 95.5% nucleotide identities, respectively (Fig. 1). Therefore, we determined our isolate to be a putative novel species in the genus Larkinella. For genome sequencing, Larkinella sp. strain BK230 cells were grown in liquid R2A medium overnight at 25°C with shaking. DNA was prepared utilizing a Qiagen DNeasy kit. The draft genome of Larkinella sp. strain BK230 was generated at the Department of Energy (DOE) Joint Genome Institute (JGI) using Illumina technology (3). An Illumina standard shotgun library was constructed and sequenced using the Illumina NovaSeq platform, which generated 12,544,362 reads, totaling 1,894,198,662 bp. Raw Illumina sequence data were quality filtered using BBTools (4), according to standard operating procedure 1061. The following steps were then performed for assembly: (i) artifact-filtered and normalized Illumina reads were assembled using SPAdes v3.12.0 (parameters were as follows: phred-offset 33, cov cutoff auto, t 16, m 64, careful, and k 25,55,95) (5); and (ii) contigs were discarded if the length was <1 kbp (BBTools reformat.sh, minlength). The final draft assembly contained 16 contigs in 15 scaffolds, totaling 7,274,818 bp. The final assembly was based on 1,497,902,613 bp of Illumina data, with a mapped coverage of 203.4×. The final genome assembly completeness (100%) and contamination (0.3%) were assessed with CheckM; a metabolic model was generated using KBase (6) and is accessible online (https://narrative.kbase.us/narrative/ws.54100.obj.1). Annotation was performed using the standard IMG Annotation Pipeline v4.16.4, resulting in 6,026 coding sequences, including 5,973 protein-coding genes and 53 RNA genes.
FIG 1
FIG 1 Neighbor-joining phylogenetic tree based on 16S rRNA sequences of Larkinella sp. strain BK230 and reference species downloaded from the NCBI database. Rudanella lutea was utilized as an outgroup. The bootstrap support values of the branches are indicated.

Data availability.

The complete draft genome sequence is available from the IMG/MER database under accession number 2802428837 and has been deposited in GenBank under accession number SODS00000000. The version described in this paper is the first version (SODS01000000). The raw sequence reads have been deposited in the SRA database under accession number SRP191027.

ACKNOWLEDGMENTS

We thank Kerrie Barry and Nicole Shapiro (JGI) for project management and Tse-Yuan Lu for help with strain isolation.
This manuscript was authored by UT-Battelle, LLC, which manages Oak Ridge National Laboratory for the U.S. DOE, under contract DE-AC05-00OR22725. Part of this research was funded by the U.S. DOE Office of Biological and Environmental Research, Genomic Science Program, as part of the Plant Microbe Interfaces Scientific Focus Area. Bellville field site maintenance was funded by the BioEnergy Science Center project. The BioEnergy Science Center is a U.S. DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the U.S. DOE Office of Science. The work conducted by the U.S. DOE JGI, a DOE Office of Science User Facility, is supported under contract DE-AC02-05CH11231. DNA sequencing and library preparation were performed as part of a JGI Community Science Program user project (project 503495) under U.C.K.

REFERENCES

1.
Utturkar SM, Cude WN, Robeson MS, Jr, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. 2016. Enrichment of root endophytic bacteria from Populus deltoides and single-cell-genomics analysis. Appl Environ Microbiol 82:5698–5708.
2.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649.
3.
Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438.
4.
Bushnell B. 2014. BBTools software package. http://bbtools.jgi.doe.gov.
5.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.
6.
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia J-M, Chia J-M, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. 2018. KBase: the United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36:566–569.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 1219 March 2020
eLocator: e00159-20
Editor: Frank J. Stewart, Georgia Institute of Technology
PubMed: 32193238

History

Received: 18 February 2020
Accepted: 27 February 2020
Published online: 19 March 2020

Contributors

Authors

Dale A. Pelletier
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Leah H. Burdick
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Mircea Podar
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Christopher W. Schadt
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Udaya C. Kalluri
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Editor

Frank J. Stewart
Editor
Georgia Institute of Technology

Notes

Address correspondence to Dale A. Pelletier, [email protected].

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

View options

PDF/ePub

PDF/ePub

Get Access

Buy Article
Microbiology Resource Announcements Vol.9 • Issue 12 • ASM Journals Pay Per View, PPV 25
Journal Subscription
Microbiology Resource Announcements
ASM members can purchase subscriptions to journals.
Join or renew

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy