Data from: Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing

Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa R, Edvardsen B

Date Published: March 18, 2015

DOI: http://dx.doi.org/10.5061/dryad.b8d21

 

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Title Environmental data for manuscript mec-14-1145
Downloaded 97 times
Description Excel-file containing environmental data from the sampling site OF-2 (59.186668N, 10.691667E), Oslofjorden, Norway, in the study period September 2009-June 2011.
Download Env_data_mec-14-1145.xlsx (49.28 Kb)
Download README.docx (137.0 Kb)
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Title Table_S2_Egge_et_al_2015_jeukmic
Downloaded 12 times
Description Table containing information about the haptophyte V4 SSU rRNA OTUs recorded in Skagerrak in the period September 2009 – June 2011. First published in Egge ES, Eikrem W, Edvardsen B (2015) “Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing”, Journal of Eukaryotic Microbiology 62, 121-140. DOI: 10.1111/jeu.12157
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Title Haptophyte_ref_alignment_284tax
Downloaded 14 times
Description Reference alignment comprising 281 haptophyte 18S rDNA sequences representing all cultured haptophyte species, environmental sequences forming novel clades, and the best BLAST hits in NCBI-nr to the Oslofjorden OTUs. Three outgroup sequences are included (AJ564771 Telonema subtilis, AY919672 Kathablepharis remigera, L28811 Chilomonas paramecium). The sequences from cultured species and environmental sequences that formed novel clades were aligned in MAFFT v.6 with the Q-INS-i strategy (Katoh and Toh 2008). BLAST hits in NCBI-nr that were not already present in the alignment were inserted into the existing alignment using the add-in function in MAFFT for full-length sequences, with method L-INS-1 (Katoh and Frith 2012).
Download Haptophyte_ref_alignment_284tax.fas (582.5 Kb)
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Title MEC-14-1145-OTUtab_piconanopool_notsubsamp
Downloaded 8 times
Description OTU table, read number not subsampled to even sampling depth.
Download MEC-14-1145-OTUtab_piconanopool_notsubsamp.xls (58.88 Kb)
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Title Table of OTU read abundance per sample, subsampled to even sampling depth.
Downloaded 8 times
Description OTU table, read number subsampled to even sampling depth (5553 reads).
Download MEC-14-1145-OTUtab_piconanopool_subsamp55...on.xls (60.92 Kb)
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Title RAxML reference tre of 281 haptophyte taxa + 3 outgroups
Downloaded 8 times
Description Maximum likelihood phylogenetic trees of 281 reference haptophyte sequences (all cultured species + selected environmental sequences) + 3 outgroups (L28811 Chilomonas paramecium, AY919672 Kathablepharis remigera, AJ564771 Telonema subtilis), constructed using RAxML v. 7.3.2 (Stamatakis 2006, Bioinformatics 22:2688-2690), with substitution model GTRCAT and 100 bootstrap runs. RAxML was run on the Lifeportal on the University of Oslo computer cluster (www.lifeportal.uio.no).
Download RAxML_haptophyte_284_taxa_reference_tree.tre (25.10 Kb)
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Title Fasta-file of 156 haptophyte OTUs.
Downloaded 8 times
Description Fasta file of 156 haptophyte OTUs, aligned (using MAFFT add-in) to the reference alignment with 281 haptophyte reference sequences.
Download MEC-14-1145-OTUs_aligned.fasta (304.7 Kb)
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When using this data, please cite the original publication:

Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa R, Edvardsen B (2015) Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Molecular Ecology 24(12): 3026-3042. http://dx.doi.org/10.1111/mec.13160

Additionally, please cite the Dryad data package:

Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa R, Edvardsen B (2015) Data from: Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.b8d21
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