Understanding Bivalve Gametogenesis

Comparative transcriptomics for bivalve gametogenesis

Subdirectory Info

code/ contains code

• 01-retrievegenomes.Rmd downloads refseq annotated Bivalvia genomes from NCBI

• 02-blastoncds.Rmd runs tblastn to find genes associated with gamete generation (uses gamete generation genes containing fasta as querey, and cds genome files for bivalve species as database)

• 03-phyluce.Rmd follows the phyluce III tutorial for harvesting UCE loci from genomes

data/ contains data

• data/SwissProt-GO:0007276.fa fasta files of all NCBI genes under gamete generation GO term

• data/genome_info-20250407.tsv NCBI table with metainfo on the refseq annotated Bivalvia genomes

• data/genomes_refseq/ has the ncbi output sequences

• data/phyluce/ contains all the data related to phyluce including:

  • .2bit genome files: GCF_#########/GCF_#########.2bit

  • UCE baits used: Baits_Bivalve_v1.fasta and Baits_Bivalve_v2.fasta

  • the lastz uce hit output files: v1-genome-lastz and v2-genome-lastz

  • fasta uce hit output files: v1-genome-fasta and v2-genome-fasta

  • uces from baits: uce_frombaits_v1 and uce_frombaits_v2

  • logs from running phyluce: phyluce.log (v1 error log) and phyluce_v2.log (v2 error log), phyluce_probe_run_multiple_lastzs_sqlite.log (lastz run log), and phyluce_probe_slice_sequence_from_genomes (lastz to fasta run log)

  • comparison of lastz and fasta bait v1 and bait v2 UCE hits: sequence_summary.csv

output/ stores outputs

• blastout/GCF_########.tab : blast output

• blastout/GCF_########_with_headers.tab : blast output with headers

• blastout/GCF_########_sep.tab : blast output with seperated entry column (to obtain SPID)

• GCF_########_SPID.txt : SwissProt ID / UniProt Accession numbers from Blast Output

• GCF_########_uniprotout : UniProt Table for that species

• GCF_########_annotation.tab : combination of BLAST table and UniProt Table for that species

• genelist_GCF_#########.csv : BLAST table and UniProt table table, but only keeps relevant columns (for brevity)

visuals/ stores visuals

blastdb/ is the blast database created when running blast