Table_S2_Egge_et_al_2015_jeukmic

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.1215

Diversity and distribution of haptophytes reavealed by environmental sequencing - a review. Perspectives in Phycology. Supplementary material.

<p><b></b> </p><p><b>7. Fig. S1. </b>Maximum-likelihood tree<b> </b>(RAxML v. 8.026, GTRCAT) based on 971 haptophyte 18S rRNA gene sequences from Table S1, 451 are from cultured strains and 520 from environmental clone libraries. Bootstrap values are marked at the nodes. The colours indicate taxonomic groups.</p> <p><b>8. Table S1. </b>Haptophyte 18S rRNA gene sequence reference database including 971 sequences, 451 from cultures and 520 from environmental clone libraries. See File S1 for description of its construction. Chimeras (32) identified by uchime in mothur and by manual blast are listed on sheet 2.</p> <p><b>9. Table S2</b>. Information on selected, commonly used PCR primers for environmental sequencing and metabarcoding of haptophytes.</p> <p><b>10. File S1.</b> Description of the construction of the Haptophyte 18S rRNA gene reference sequence database, alignment and final RAxML phylogenetic tree.</p> <p><b>11. File S2. </b>Fasta file with accession numbers and 18S rRNA gene sequence of 971 reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>12. File S3. </b>Taxonomy file with systematic placement of 971 haptophyte reference sequences for taxonomic assignment in mothur or Qiime. </p> <p><b>13. File S4. </b>Curated haptophyte 18S rRNA gene alignment for Figs 2 and S1.</p

Table of OTU read abundance per sample, subsampled to even sampling depth.

OTU table, read number subsampled to even sampling depth (5553 reads)

Fasta-file of 156 haptophyte OTUs.

Fasta file of 156 haptophyte OTUs, aligned (using MAFFT add-in) to the reference alignment with 281 haptophyte reference sequences

Haptophyte_ref_alignment_284tax

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)

Environmental data for manuscript mec-14-1145

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

RAxML reference tre of 281 haptophyte taxa + 3 outgroups

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)