This narrative was used for a complete genome sequence of a Starkeya species, an alphaproteobacterium. Other members of the genus have been identified in soil samples and rice straw1-4. This publication sequences an example isolated from a rhizosphere of a Populus deltoides tree in Oak Ridge, TN.
The publication by Mircea Podar, Joel Turner, Leah H. Burdick, and Dale A. Pelletier can be found here: https://mra.asm.org/content/9/27/e00644-20
Narrative created by Mircea Podar, edited by Zachary Crockett
An assembly and Genbank genome of the close relative, S. novella, were also imported for ocmparison.
CheckM was run on the assembled reads to verify quality control.
The RAST algorithm was applied to annotating a genome sequence comprised of 1 contigs containing 6286191 nucleotides. No initial gene calls were provided. Standard features were called using: glimmer3; prodigal. A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr. The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity. In addition to the remaining original 0 coding features and 0 non-coding features, 6254 new features were called, of which 199 are non-coding. Output genome has the following feature types: Coding gene 6055 Non-coding repeat 146 Non-coding rna 53 Overall, the genes have 2752 distinct functions. The genes include 2719 genes with a SEED annotation ontology across 1316 distinct SEED functions. The number of distinct functions can exceed the number of genes because some genes have multiple functions.