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Datasets

The Santos Lab is happy to offer downloadable datasets and sequence alignments of molecules commonly utilized in Symbiodinium diversity and phylogenetic studies. These alignments are for use as a scaffold to which novel sequences may be added and preliminary phylogenies constructed. Given the rate that new sequences are generated, these alignments are not representative of all sequences available from sources such as NCBI, and are not intended to encompass all Symbiodinium diversity (either within the genus or any particular clade). The alignments are made available in NEXUS format (for use in programs such as PAUP*) and can be converted to other formats using the program seqret in EMBOSS Explorer. If a sequence in the alignment does not have a NCBI accession number (most don't), you can use SYM-BLAST to identify it. To download a file, right-click the link and save it to your computer. For additional sequence alignments of molecules commonly used in Symbiodinium phylogenetics, you may also want to check the NCBI PopSet and TreeBase databases.

 

Clade A

Clade B

Clade C

All Clades (A/B/C/D/E/F/G/H)

 18S-rDNA

 Download

 Download

 Download

 Download

 28S-rDNA

 Download

 Download

 Download

 Download

 cp23S-rDNA

 Download

 Download

 Download

 Download

 ITS2-rDNA

 Download

 Download

 Download

 Download

 Hunter et al. ITS2

 Download

 Download

 Download

 Download

 5.8S-rDNA

 -

 -

 -

 Download

 COI

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 -

 -

 Download

 psbA

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 -

 -

 Download

 Microsatellite CA4.86

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 Download

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 Microsatellite CA6.38

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 Download

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Other Datasets

Malacostraca complete mitochondrial sequences: Nucleotide and amino acid alignments utilized in Ivey and Santos (2007) Gene 394:35-44. Zip Archive

Symbiodinium ITS intragenomic data: alignments and chromatograms from Thornhill et al. (2007) Molecular Ecology 16:5326-5340. Zip Archive (46 MB)

Symbiodinium microsatellite data: files for computational analysis via Structure of Symbiodinium Clade B populations from Gorgonia ventalina in the Florida Keys utilized in Kirk et al. (2009) Marine Biology 156:1609-1623. Zip Archive

Symbiodinium microsatellite data: colony info, allelic variation and AMOVA hierarchical structure for analyses with GenAlEx from Symbiodinium Clade B populations of M. faveolata and M. annularis from Thornhill et al. (2009) PLoS One 4:e6262. Zip Archive

Montastrea spp. mitochondrial sequence data: Nucleotide alignments of the mtDNA intergenic region for M. faveolata and M. annularis from the Florida Keys and Bahamas utilized in Thornhill et al. (2010) Marine Ecology Progress Series 420:113-123. Zip Archive

Coral-associated apicomplexan sequence data for various coral species from Kirk et al. (2013) Coral Reefs 32:847-858. Zip Archive

Coral-associated apicomplexan sequence data for brooding vs. broadcast-spawning coral species from Kirk et al. (2013) PLoS One 8:e80618. Zip Archive

Mitogenome amino acid (AA) and nucleotide (nt) alignments, tree files, and scripts used in Havird and Santos (2014) PLoS One 9:e84080. NOTE: the archive is ~20 GB in size when compressed with 7Zip and will expand into a directory of ~120 GB. If you would like a subset of the data without downloading the whole archive, please contact Justin C. Havird directly. 7Zip Archive

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