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.