Rickettsia Presence in Arthropod Whole Genome Projects from SRA

Insights into Rickettsia symbioses were obtained by screening 60,409 Illumina datasets from arthropod whole genome sequence projects in the Sequence Read Archive as of May 20, 2019. The data was processed with phyloFlash to extract Rickettsia 16S rRNA sequences and Kraken2 for microbial composition analysis. This dataset was created by Stefanos Siozios and is available under an Open Access license.

Use Cases

• Phylogenetic placement of Rickettsia sequences based on reconstructed 16S rRNA genes.
• Assessing group representation of Rickettsia within arthropod symbioses based on SRA dataset screening.
• Identifying potential Rickettsia infections using a Kraken2-based taxonomic classifier with a read count threshold.
• Mitigating bias from over-represented laboratory model species by analyzing a single, largest dataset per species.

Strengths

• Analysis is based on 60,409 SRA records associated with arthropod whole genome projects.
• A bias-reduction strategy was applied by examining a single dataset with the largest read count per species.
• A specific cut-off of at least 40k reads assigned to Rickettsia was used for reporting potential infections.

Limitations

• Row count and column-level documentation are unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.
• The dataset's temporal coverage is a snapshot as of a specific date in 2019.

Provenance

Source

Sequence Read Archive (SRA) arthropod whole genome sequence projects.

Collection Method

Datasets were screened with phyloFlash for 16S rRNA sequences and Kraken2 for taxonomic classification.

Time Range

Snapshot as of May 20, 2019.