Biological samples |
|
Aequorea sp. |
This study |
ZRC.CNI.1440 |
Phyllorhiza punctata |
This study |
ZRC.CNI.1437 |
Zygocanna sp. |
This study |
ZRC.CNI.1433 |
Acromitus sp. |
This study |
ZRC.CNI.1396 |
Phyllorhiza punctata |
This study |
ZRC.CNI.1439 |
Acromitus sp. |
This study |
ZRC.CNI.1436 |
Cassiopea sp. |
This study |
ZRC.CNI.3022 – ZRC.CNI.3023 |
Morbakka sp. |
This study |
ZRC.CNI.1418 |
|
Critical commercial assays |
|
E.Z.N.A.® Mollusc DNA Kit |
Omega Bio-Tek |
D3373 |
Genomic DNA Clean & Concentrator – 25 |
Zymo Research |
D4065 |
KAPA HyperPrep Kit |
KAPA Biosystems |
KK8502 |
|
Deposited data |
|
Raw reads of Medusozoa samples |
This study |
NCBI SRA BioProject PRJNA934731 |
Aequorea sp. mitogenome |
This study |
GenBank: OR400200
|
Phyllorhiza punctata mitogenome |
This study |
GenBank: OR400201
|
Zygocanna sp. mitogenome |
This study |
GenBank: OR400202
|
Acromitus sp. mitogenome |
This study |
GenBank: OR400203
|
Phyllorhiza punctata mitogenome |
This study |
GenBank: OR400204
|
Acromitus sp. mitogenome |
This study |
GenBank: OR400205
|
Cassiopea sp. mitogenome |
This study |
GenBank: OR400206
|
Morbakka sp. mitogenome |
This study |
GenBank: OR400207 – OR400214
|
84 publicly available Cnidaria mitogenome sequences |
NCBI GenBank |
Refer to Tables S2 and S3
|
|
Software and algorithms |
|
fastp v0.23.2 |
Chen et al., 201870
|
https://github.com/OpenGene/fastp |
SPAdes v3.15.4 |
Bankevich et al., 201271
|
https://cab.spbu.ru/software/spades/ |
BLAST v2.90 |
Camacho et al., 200972
|
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ |
NOVOplasty v4.3.1 |
Dierckxsens et al., 201773
|
https://github.com/ndierckx/NOVOPlasty |
minimap2 v2.17-r941 |
Li, 201874
|
https://github.com/lh3/minimap2 |
Samtools v1.13 |
Danecek et al., 202175
|
https://www.htslib.org/ |
Geneious Prime v2022.0.1 |
Kearse et al., 201276
|
https://www.geneious.com/ |
Inverted Repeats Finder v3.08 |
Warburton et al., 200477
|
https://tandem.bu.edu/irf/home |
IUPACpal |
Alamro et al., 202178
|
https://sourceforge.net/projects/iupacpal/ |
MITObim v1.9 |
Hahn et al., 201379
|
https://github.com/chrishah/MITObim |
MITOS2 |
Bernt et al., 201380
|
http://mitos2.bioinf.uni-leipzig.de/index.py |
Infernal cmscan v1.1.2 |
Nawrocki & Eddy, 201381
|
http://eddylab.org/infernal/ |
tRNAscan-SE v2.0 |
Chan et al., 202182
|
http://lowelab.ucsc.edu/tRNAscan-SE/ |
MAFFT v7.453 |
Katoh & Standley, 201384
|
https://mafft.cbrc.jp/alignment/server/index.html |
TranslatorX |
Abascal et al., 201086
|
http://translatorx.co.uk/ |
Gblocks v0.91b |
Talavera & Castresana, 200749
|
http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks |
ModelTest-NG v0.2.0 |
Darriba et al., 201987
|
https://github.com/ddarriba/modeltest |
RAxML-NG v0.8.1 |
Kozlov et al., 201988
|
https://github.com/amkozlov/raxml-ng |
PhyloBayes v3.3e |
Lartillot et al., 200951
|
https://github.com/bayesiancook/phylobayes |
Tracer v1.7.1 |
Rambaut et al., 201889
|
http://beast.community/tracer |
TreeRex v1.85 |
Bernt et al., 200890
|
https://siks.informatik.uni-leipzig.de/185-0-TreeREx.html |