This narrative was used for a draft genome of a Larkinella species. This genus contains 9 identified species, of which only 5 have genome sequence data. This specimen was collected from a root sample of an eastern cottonwood (Populus deltoides) from a fied site in Bellville, Georgia.
The publication by Dale A. Pelletier, Leah H. Burdick, Mircea Podar, Christopher W. Schadt, Udaya C. Kalluri can be found here: https://mra.asm.org/content/9/12/e00159-20.abstract
Narrative created by Dale Pelletier, edited by Zachary Crockett
Washed root tissue was ground, diluted, and plated on Reasoner's 2A agar and incubated for 7 days at 25°C.
For genome sequencing, cells were grown in R2A medium overnight at 25°C.
An Illumina standard shotgun library was constructed, consisting of 12,544,362 reads totaling 1,894,198,662 bp.
The final draft assembly contained 16 contigs totaling 7,274,818 bp based on 1,497,902,613 bp of Illumina data with 203.4x coverage.
A metabolic model was constructed in KBase, shown below.
The RAST algorithm was applied to annotating a genome sequence comprised of 15 contigs containing 7274818 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, 6463 new features were called, of which 191 are non-coding. Output genome has the following feature types: Coding gene 6272 Non-coding crispr_array 1 Non-coding crispr_repeat 66 Non-coding crispr_spacer 65 Non-coding repeat 12 Non-coding rna 47 Overall, the genes have 2244 distinct functions. The genes include 2883 genes with a SEED annotation ontology across 999 distinct SEED functions. The number of distinct functions can exceed the number of genes because some genes have multiple functions.