The Cockroach UCE Database

The Cockroach UCE Database. Centralization of cockroaches UCE data and assignation of unique identification code.

This database is maintained by the Evolutionary Genomics Unit at OIST.

For any question or request, please open an issue.

A/ Referenced contributions of UCE data

Listed contributions to the Database.

Contribution	Number of samples	Reference	Data location
#1	61	Kovacs et al. Syst Biol	Dryad

Since 2024, command-line direct download is prevented for non-browser access. You can either use the links of each contribution and download them one-by-one using your favorite internet navigator. Datasets can still be accessed by mimicking browser access through --user-agent option of wget (e.g., wget --user-agent="Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7)") as suggested on this StackExchange post. Note that --user-agent needs to be changed after each use. For a more permanent solution, you can install a random user-agent generator, such as randomua written in ruby (to be installed with the command: gem install randomua).

B/ Methods and suggested database usage

For general documentation, refer to same section on the Termite UCE Database (TER-UCE-DB), at:

Updated codes within each sub-section are provided below.

B.1. Extraction of UCEs from newly-generated assemblies

The set of 319,243 baits targeting 30,059 UCE loci is available from Dryad (File: roaches-v1-master-probe-list-DUPE-SCREENED.fasta.gz). This bait set was designed using six genomes:

• three publicly available genomes: Blatella germanica (GenBank accession no. GCA_003018175.1), Periplaneta americana (GCA_002939525.1), and the termite Zootermopsis nevadensis (GCF_000696155.1);
• three in-house genomes: Geoscapheus dilatatus, Neogeoscapheus hanni, and Panesthia cribrata.

For details on the design, refer to the Supplementary Material on Zenodo.

### 1. Get the baits
### Note (2024): randomua is used for terminal access (see section A)
## Dryad: roaches-v1-master-probe-list-DUPE-SCREENED.fasta.gz
wget --user-agent="$(randomua -d)" https://datadryad.org/stash/downloads/file_stream/2761879 --output-document=roaches-v1-master-probe-list-DUPE-SCREENED.fasta.gz && gzip -d roaches-v1-master-probe-list-DUPE-SCREENED.fasta

B.2. Leveraging the database

### 5. Generate the database
### Note (2024): randomua is used for terminal access (see section A)
## Contribution #1
wget --user-agent="$(randomua -d)" https://datadryad.org/stash/downloads/file_stream/2761883 --output-document=ROA_UCE_DB_CONTRIB_1.fasta.gz && gzip -d ROA_UCE_DB_CONTRIB_1.fasta.gz

C/ How to cite

Kovacs, T.G.L, Walker, J., Hellemans, S., Bourguignon, T., Tatarnic, N.J., McRae, J.M., Ho, S.Y.W, Lo, N. 2024. Dating in the dark: elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates. Systematic Biology 73: 532–545. doi: 10.1093/sysbio/syae002

[Preprint on bioRxiv 2023.01.17.524483]