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
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.