Draft Genome Sequence of Exiguobacterium indicum strain LL15 from a urban freshwater lake in Northern Kentucky

Elisha J. Redman and Joshua T. Cooper ORCID

Department of Biological Sciences, Northern Kentucky University, 1 Nunn Drive, Highland Heights, KY 41099, USA

Introduction

Exiguobacterium indicum has often reported from a wide variety of environmental samples, ranging from extreme to common habitats^1,². Here we report the 3.1-Mb draft genome of E. indicum strain LL15, discovered during an investigation of freshwater lakes in residential-urban environments.

External Data Availability

The data were deposited in the Sequence Read Archive (SRA) as SRR19987099 under BioProject PRJNA734631, and BioSample SAMN28844364.
This Whole Genome Shotgun project has been deposited at GenBank under the accession JANFNX000000000. The version described in this paper is version JANFNX010000000.
Linked publication:

The publication may not be available at the time of the static Narrative creation. This can be added after the fact; please contact [email protected] to update the DOI landing page when this is done.

from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "31e93066beb421a51b9c8e44b1201aa93aea0b4e",
        "params": [{
            "fastq_fwd_staging_file_name": "LL15_S182_R1_001.fastq.gz",
            "fastq_rev_staging_file_name": "LL15_S182_R2_001.fastq.gz",
            "name": "LL15reads",
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }]
    }],
    cell_id="25ece73e-368d-46da-90ef-3fa85fffcf88",
    run_id="d3c5920f-acd6-4914-820f-d39065521349"
)

Background and Experimental Methods

Sample Collection

Exiguobacterium indicum, strain LL15 was isolated from Camp Ernst Lake in Burlington, KY using a sterile WhirlPak bag on a surface level grab.

Isolation

The water sample was serially diluted and spread onto tryptic soy agar (TSA) and was then incubated for 48 hours at 25°C. Individual colonies were purified to single isolates on TSA media using the quadrant streak method

Genome Sequencing

Genomic DNA was isolated using the UltraClean® Microbial DNA Isolation Kit (Qiagen, Maryland, USA) from tryptic soy broth inoculated from an isolated colony. DNA was quantified using the Qubit 3.0 Broad Range Kit (Invitrogen) and the sample was sequenced at the Microbial Genome Center (MiGS, University of Pittsburgh, PA), using the Illumina Nextera chemistry, as 150 base paired-end reads on the Illumina NextSeq 2000. Raw data were processed using the KBase v2.3.2 ³ web interface from quality control to genome assembly using default settings unless otherwise noted. Reads were quality controlled using FastQC v0.119 ⁴, and then trimmed with Trimmomatic v0.36 ⁵ and Nextera Adapters. The genome was assembled using SPAdes v3.15.3 ⁶ , a de Bruijn graph assembler into 10 contigs, with a total length of 3,102,801 bp, and an N50 of 2,120,415 bp. CheckM v1.0.18 ⁷ was used to estimate the genome completeness and contamination. The genome of species LL15 was 99.34% complete and had 0.0% contamination.

QC, Assembly, and Annotation

Raw data were processed using the KBase v2.3.2 web interface from quality control to genome assembly using default settings unless otherwise noted. Reads were quality controlled using FastQC v0.119, and then trimmed with Trimmomatic v0.36 and Nextera Adapters.

The genome was assembled using SPAdes v3.15.3 , a de Bruijn graph assembler into 10 contigs, with a total length of 3,102,801 bp, and an N50 of 2,120,415 bp. CheckM v1.0.18 was used to estimate the genome completeness and contamination. The genome of species LL15 was 99.34% complete and had 0.0% contamination.

Proteins were initially predicted using RASTtk v1.073 and Prokka v1.14.5. NCBI Prokaryotic Genome Annotation⁸ was used to make the final protein predictions to be compliant with GenBank submission.

Taxonomic Identification

References

Chaturvedi P, Shivaji S. 2006. Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India. International Journal of Systematic and Evolutionary Microbiology 56:2765–2770.
Dastager SG, Mawlankar R, Sonalkar VV, Thorat MN, Mual P, Verma A, Krishnamurthi S, Tang S-K, Li W-J. 2015. Exiguobacterium enclense sp. nov., isolated from sediment. International Journal of Systematic and Evolutionary Microbiology 65:1611–1616.
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. 7. Nat Biotechnol 36:566–569.
FastQC source: Bioinformatics Group at the Babraham Institute, UK. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114 2120. doi:10.1093/bioinformatics/btu170
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology. 2012;19: 455-477. doi: 10.1089/cmb.2012.0021
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. 14. Nucleic Acids Res 44:6614–6624.

Created Object Name	Type	Description
LL15reads_trim_paired	PairedEndLibrary	Trimmed Reads
LL15reads_trim_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
LL15reads_trim_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
SPAdes.Assembly_DRAM	Genome	Annotated Genome
Dram_Assembly	GenomeSet	LL15_Dram