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. 2023 Oct 18;26(11):108252. doi: 10.1016/j.isci.2023.108252
REAGENT or RESOURCE SOURCE IDENTIFIER
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