Here you can find fasta and gff files of branchiopod Hox and ParaHox genes (HPHGs), organized as follow:
01_HPHG_seqs/amino_acid_seqs/hosts fasta files of amino acid sequences;01_HPHG_seqs/nucleotide_seqs/hosts fasta files of nucleotide sequences;02_HPHG_gffs/hosts gff files.
Supplementary data and materials can be found in this GitHub repository.
Headers for each fasta file contained in this repository are formatted as follow: >spID_gene.acc.no_geneID. spIDs can be found in the next section or in the genome_table.tsv file. gene.acc.nos are the same as in the annotation. geneIDs are as follow:
- labial: lab
- proboscipedia: pb
- Hox-3: hox3
- deformed: dfd
- sex-comb reduced: scr
- fushi tarazu: ftz
- antennapedia: antp
- ultrabithorax: ubx
- abdominal-A: abdA
- abdominal-B: abdB
- caudal: cad
- intermediate neuroblasts defective: ind
- pancreatic-duodenal homeobox: Pdx
- even-skipped: eve
Here are the genome assemblies from which HPHGs were extracted. For each of them, the species ID and the link to the source website are provided. The same information, but parsable, can be found in the genome_table.tsv file.
- Drosophila melanogaster (Dmel, GCF_000001215.4)
- Folsomia candida (Fcan, GCF_002217175.1)
- Artemia franciscana (Afr1, Korea Polar Research Institute)
- Daphnia magna (Dmag, GCF_003990815.1)
- Daphnia pulex (Dpul, GCA_000187875.1)
- Eulimnadia texana (Etex, GCA_002872375.1)
- Leptestheria dahalacensis (Ldah, GCA_022114935.1)
- Lepidurus apus lubbocki (Lubb, GCA_003723985.1)
- Lepidurus apus apus (Lapu, GCA_022832285.1)
- Lepidurus arcticus (Lart, GCA_003724045.1)
- Lepidurus couesii (Lcou, GCA_022832235.1)
- Triops longicaudatus (Tlon, GCA_022885665.1)
- Triops cancriformis IT (Tcit, GCA_022832245.1)
- Triops cancriformis ES (Tces, GCA_022832265.1)