DOI: 10.5061/dryad.rj87v
title: Data from: Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista

description: Assembling the global eukaryotic tree of life has long been a major effort
 of Biology. In recent years, pushed by the new availability of
 genome-scale data for microbial eukaryotes, it has become possible to
 revisit many evolutionary enigmas. However, some of the most ancient
 nodes, which are essential for inferring a stable tree, have remained
 highly controversial. Among other reasons, the lack of adequate genomic
 datasets for key taxa has prevented the robust reconstruction of early
 diversification events. In this context, the centrohelid heliozoans are
 particularly relevant for reconstructing the tree of eukaryotes because
 they represent one of the last substantial groups that was missing large
 and diverse genomic data. Here, we filled this gap by sequencing
 high-quality transcriptomes for four centrohelid lineages, each
 corresponding to a different family. Combining these new data with a broad
 eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic
 dataset that enabled us to refine the structure of the tree. Specifically,
 we show that (i) centrohelids relate to haptophytes, confirming Haptista;
 (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with
 Archaeplastida; and (iv) Haptista + SAR is sister to Cryptista +
 Archaeplastida. The implications of this topology are discussed in the
 broader context of plastid evolution.
description: Transcriptome assembly
 of Amastigomonas spRNA-seq assembly of
 Amastigomonas sp. from Genbank SRA accession #SRR2170627. Read quality was
 assessed with FastQC before and after quality trimming and SMART adaptors
 removal, which was performed with FastqMcf. Cleaned reads were assembled
 into contigs with Trinity r20140717 using default
 parameters.Amastigomonas_sp_transcriptome.fasta.zipTranscriptome assembly of Raineriophrys erinaceoidesRNA-seq assembly of Raineriophrys erinaceoides from Genbank SRA accession #SRR2170634. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters.Raineriophrys_erinaceoides_transcriptome.fasta.zipTranscriptome assembly of Choanocystis spRNA-seq assembly of Choanocystis sp. from Genbank SRA accession #SRR2170626. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parametersChoanocystis_sp_transcriptome.fasta.zipTranscriptome assembly of Acanthocystis spRNA-seq assembly of Acanthocystis sp. from Genbank SRA accession #SRR2170625. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parametersAcanthocystis_sp_transcriptome.fasta.zipTranscriptome assembly of Raphidiophrys heterophryoideaRNA-seq assembly of Raphidiophrys heterophryoidea from Genbank SRA accession #SRR2170621. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parametersRaphidiophrys_heterophryoidea_transcriptome.fasta.zipTrimmed alignmentTrimmed alignment of all 250 genes. BMGE was used for trimming, following MAFFT-LINSI for automatic alignment.fasta_trimmed.zipUntrimmed sequencesFasta files of all 250 genes containing untrimmed sequences.fasta_untrimmed.zipSingle-gene phylogenetic treesRAxML phylogenetic trees of all 250 genes.trees.zip