All complete bottlenose mitochondria available from NCBI (link) were downloaded to ./all.ncbi.complete.bottlenose.mito.fa. The follow search criteria were used in NCBI’s Nucleotide database to retrieve the mitochondrial sequences:
txid9739[Organism:exp] AND
(is_nuccore[filter] AND
mitochondrion[filter] AND
("16000"[SLEN] : "17000"[SLEN]))
| Accession | Location |
|---|---|
| CM022296.1 | Unknown |
| NC_012059.1 | Unknown |
| MF669486.1 | BSEA |
| MF669485.1 | BSEA |
| EU557093.1 | Unknown |
| KT601207.1 | ENAP |
| KT601206.1 | ENAP |
| KT601205.1 | ENAP |
| KT601204.1 | ENAP |
| KT601203.1 | ENAP |
| KT601202.1 | ENAP |
| KT601201.1 | ENAP |
| KT601200.1 | ENAP |
| KT601199.1 | ENAP |
| KT601198.1 | ENAP |
| KT601197.1 | ENAP |
| KT601196.1 | ENAC |
| KT601195.1 | ENAC |
| KT601194.1 | ENAC |
| KT601193.1 | ENAC |
| KT601192.1 | ENAC |
| KT601191.1 | ENAC |
| KT601190.1 | ENAC |
| KT601189.1 | ENAC |
| KT601188.1 | ENAC |
| KF570389.1 | GC |
| KF570388.1 | WNAP |
| KF570387.1 | WNAP |
| KF570386.1 | WNAP |
| KF570385.1 | WNAP |
| KF570384.1 | WNAP |
| KF570383.1 | WNAP |
| KF570382.1 | WNAP |
| KF570381.1 | WNAP |
| KF570380.1 | WNAP |
| KF570379.1 | WNAP |
| KF570378.1 | WNAC |
| KF570377.1 | WNAC |
| KF570376.1 | WNAC |
| KF570375.1 | WNAC |
| KF570374.1 | WNAC |
| KF570373.1 | WNAC |
| KF570372.1 | WNAC |
| KF570371.1 | WNAC |
| KF570370.1 | WNAC |
| KF570352.1 | SCO |
| KF570351.1 | SCO |
| KF570350.1 | SCO |
| KF570349.1 | SCO |
| KF570348.1 | SCO |
| KF570347.1 | SCO |
| KF570346.1 | SCO |
| KF570345.1 | SCO |
| KF570334.1 | BSEA |
| KF570333.1 | BSEA |
| KF570332.1 | BSEA |
| KF570331.1 | BSEA |
| KF570330.1 | BSEA |
| KF570329.1 | BSEA |
| KF570328.1 | BSEA |
| KF570327.1 | BSEA |
| KF570326.1 | BSEA |
| KF570325.1 | BSEA |
| KF570324.1 | EMED |
| KF570323.1 | EMED |
| KF570322.1 | EMED |
| KF570321.1 | EMED |
| KF570320.1 | EMED |
| KF570319.1 | EMED |
| KF570318.1 | EMED |
| KF570317.1 | EMED |
| KF570316.1 | EMED |
| KF570315.1 | EMED |
| Location | Color |
|---|---|
| Unknown | black |
| BSEA | skyblue |
| EMED | blueviolet |
| ENAC | brown4 |
| ENAP | burlywood4 |
| GC | #FFB30F |
| SCO | chartreuse4 |
| WNAC | #437F97 |
| WNAP | #01295F |
for acc in "${!accs[@]}"; do
printf "%s\t%s\n" $acc ${accs[$acc]}
donefor acc in "${!accs[@]}"; do
printf "%s\t%s\n" $acc ${colors["${accs[$acc]}"]}
doneAll complete marine dolphin mitochondrial genomes from RefSeq were downloaded to ./marine_dolphin.refseq.fasta.
| Accession | Species |
|---|---|
| NC_050265.1 | Lagenorhynchus acutus |
| NC_045404.1 | Sousa teuszii |
| NC_042761.1 | Steno bredanensis |
| NC_037848.1 | Lagenodelphis hosei |
| NC_036415.1 | Delphinus delphis |
| NC_035426.1 | Lagenorhynchus obliquidens |
| NC_032301.1 | Stenella longirostris |
| NC_019578.2 | Globicephala macrorhynchus |
| NC_023889.1 | Orcinus orca |
| NC_022805.1 | Tursiops australis |
| NC_020696.1 | Cephalorhynchus heavisidii |
| NC_019591.1 | Orcaella heinsohni |
| NC_019590.1 | Orcaella brevirostris |
| NC_019589.1 | Peponocephala electra |
| NC_019588.1 | Feresa attenuata |
| NC_019577.1 | Pseudorca crassidens |
| NC_019441.1 | Globicephala melas |
| NC_005278.1 | Lagenorhynchus albirostris |
| NC_012062.1 | Grampus griseus |
| NC_012059.1 | Tursiops truncatus |
| NC_012051.1 | Stenella attenuata |
| NC_012061.1 | Delphinus capensis |
| NC_012058.1 | Tursiops aduncus |
| NC_012057.1 | Sousa chinensis |
| NC_012053.1 | Stenella coeruleoalba |
PATH=~/.local/edirect/:$PATH
IFS=,
efetch -db nuccore -id "${accessions[*]}" -format fasta \
> marine_dolphin.refseq.fasta- Create database from marine dolphins
ml singularity/3.5.2 blast makeblastdb -dbtype nucl -in $DIR/marine_dolphin.refseq.fasta
Accession NC_012059.1 (NCBI) downloaded to ./bottlenose.mito.fa
- Split mito into amplicon sequences
ml singularity/3.5.2 samtools minimap2 declare -A primers primers['P4']="NC_012059.1:2481-9486" primers['P6']="NC_012059.1:9460-15825" primers['P7']="NC_012059.1:15418- NC_012059.1:1-5137" primers['P10']="NC_012059.1:6906-13015" for primer in "${!primers[@]}"; do samtools faidx $DIR/bottlenose.mito.fa ${primers[$primer]} | sed '/>/d' | tr -d '\n' | cat <(printf '\n>%s\n' $primer) - | fold done > $DIR/mito.amplicon.fa minimap2 -d $DIR/mito.amplicon.{mmi,fa} samtools faidx $DIR/mito.amplicon.fa