Data from: Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista

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.

Usage notes

Transcriptome assembly of Amastigomonas sp RNA-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.zip Transcriptome assembly of Raineriophrys erinaceoides RNA-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.zip Transcriptome assembly of Choanocystis sp RNA-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 parameters Choanocystis_sp_transcriptome.fasta.zip Transcriptome assembly of Acanthocystis sp RNA-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 parameters Acanthocystis_sp_transcriptome.fasta.zip Transcriptome assembly of Raphidiophrys heterophryoidea RNA-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 parameters Raphidiophrys_heterophryoidea_transcriptome.fasta.zip Trimmed alignment Trimmed alignment of all 250 genes. BMGE was used for trimming, following MAFFT-LINSI for automatic alignment. fasta_trimmed.zip Untrimmed sequences Fasta files of all 250 genes containing untrimmed sequences. fasta_untrimmed.zip Single-gene phylogenetic trees RAxML phylogenetic trees of all 250 genes. trees.zip