DOI: 10.5061/dryad.n5g39d7
title: Data from: Hemimastigophora is a novel supra-kingdom-level lineage of Eukaryotes

description: Almost all eukaryote life forms have now been placed within one of five to
 eight supra-kingdom-level groups using molecular phylogenetics1,2,3,4. The
 ‘phylum’ Hemimastigophora is probably the most distinctive morphologically
 defined lineage that still awaits such a phylogenetic assignment. First
 observed in the nineteenth century, hemimastigotes are free-living
 predatory protists with two rows of flagella and a unique cell
 architecture5,6,7; to our knowledge, no molecular sequence data or
 cultures are currently available for this group. Here we report
 phylogenomic analyses based on high-coverage, cultivation-independent
 transcriptomics that place Hemimastigophora outside of all established
 eukaryote supergroups. They instead comprise an independent
 supra-kingdom-level lineage that most likely forms a sister clade to the
 ‘Diaphoretickes’ half of eukaryote diversity (that is, the ‘stramenopiles,
 alveolates and Rhizaria’ supergroup (Sar), Archaeplastida and Cryptista,
 as well as other major groups). The previous ranking of Hemimastigophora
 as a phylum understates the evolutionary distinctiveness of this group,
 which has considerable importance for investigations into the deep-level
 evolutionary history of eukaryotic life—ranging from understanding the
 origins of fundamental cell systems to placing the root of the tree. We
 have also established the first culture of a hemimastigote (Hemimastix
 kukwesjijk sp. nov.), which will facilitate future genomic and
 cell-biological investigations into eukaryote evolution and the last
 eukaryotic common ancestor.
description: Light microscopy images
 of Hemimastix and SpironemaRaw light microscopy
 images of Hemimastix kukwesjijk and Spironema cf. multiciliatum, as used
 in paper.1_LM images Hemimastix and
 Spironema.zipSEM images Hemimastix
 kukwesjijkRaw Scanning Electron
 Microscopy images of Hemimastix kukwesjijk, as used in figures in
 paper.2_SEM
 images Hemimastix.zipSSU alignment and tree
 of HemimastigophoraEukaryote-wide small
 subunit rDNA (SSU) dataset, including Hemimastigophora kukwesjijk and
 Spironema cf. multiciliatum. Includes alignment in fasta-format and final
 RAxML-derived tree in NEWICK-format.3_SSU
 rDNA.zipTranscriptome assemblies
 of HemimastigophoraAssemblies of Hemimastix
 kukwesjijk and Spironema cf. multiciliatum transcriptomes, assembled with
 Trinity, and cleaned of cross-contamination using a custom script.
 Nucleotide-data, in fasta-format.4_transcriptome_assemblies.zipSingle gene alignments for phylogenomic dataset351 single-gene alignments used in phylogenomic analyses, aligned with MAFFT L-INS-I, untrimmed. This dataset includes 104 eukaryote taxa. In fasta-format.5_individual gene alignments.zipConcatenated alignments containing HemimastigophoraConcatenated alignments of 351-gene dataset, containing Hemimastigophora, as used in phylogenomic analyses. Trimmed with BMGE, in fasta-format. See README-file for additional information.6_concatenated alignments.zipTree files of phylogenomic analysesTree files in NEWICK-format of all phylogenomic analyses conducted. See "6_Concatenated alignments" for associated alignment data. See README-file for additional information.7_tree files.zipNon-universal ancient eukaryote genesAlignments (trimmed and untrimmed fasta-files) and tree-files (NEWIC) of non-universal ancient genes found in Hemimastigophora. See README-file for additional information.8_eukaryote_genes.zip