DOI: 10.5061/dryad.cfxpnvxfg
title: Data from: Phylogenomic diversity of archigregarine apicomplexans

description: Gregarines are a large and diverse subgroup of Apicomplexa, a lineage of
 obligate animal symbionts including pathogens like Plasmodium, the malaria
 parasite. Unlike Plasmodium, however, gregarines are poorly studied,
 despite the fact that as early-branching apicomplexans they are crucial to
 our understanding of the origin and evolution of all apicomplexans and
 their parasitic lifestyle. Exemplifying this, the earliest branch of
 gregarines, the archigregarines, are particularly poorly studied: around
 80 species have been described from marine invertebrates, but almost all
 of them were assigned to a single genus, Selenidium. Most are known only
 from light micrographs and largely unresolved rDNA phylogenies, where they
 exhibit a great deal of sequence variation, but fall into at least five
 subclades. To resolve the relationships within archigregarines, we
 sequenced 12 single-cell transcriptomes from species representing all four
 known subclades, as well as one blastogregarine (which frequently branch
 with Selenidium). A 190-gene phylogenomic tree confirmed
 fourmaximally-supported individual clades of archigregarines and
 blastogregarines. These clades are discrete and distantly related, and
 also correlate with host identity. We propose the establishment of three
 novel genera of archigregarines to reflect their phylogenetic diversity
 and host range, and nine novel species isolated from a range of marine
 invertebrates.
description: # Phylogenomic diversity of archigregarine apicomplexans These are
 supplemental data for the publication "Phylogenomic diversity of
 archigregarine apicomplexans", in Royal Society Open Biology. This
 dataset contains the assembled single-cell transcriptomes of 11
 archigregarine and one blastogregarine taxa. These assemblies were used to
 reconstruct a 190-gene phylogeny of Apicomplexa, which shows
 archigregarines and blastogregarines are composed of five independent
 clades branching sister to other gregarines. All single-gene data used to
 construct the multigene phylogeny, as well as concatenations are included,
 as are SSU rRNA gene phylogeny data. Treefiles are openable with FigTree
 or other tree-viewing software. ##### Sequenced archigregarines and
 blastogregarines: *Devanium cincinnus* Ph216 *Devanium robustum* SelFal
 *Lunidium laculatum* SNEK *Lunidium melongena* SelMel *Lunidium
 proboscidis* SNEKD *Lunidium shako* KNOB *Metzidium perlucensae* SQU2901
 *Selenidium capillus* Ph213 *Selenidium natalis* SEL2980 *Selenidium
 pherusae* Ph226 *Selenidium validusae* WK *Siedleckia leitoscoloplosis*
 BL3 ## Description of the data and file structure There are 5 main parts
 to this dataset: 1. Assemblies of 11 archigregarines and 1
 blastogregarine. In nucleotide format (ending in .fasta; generated with
 rnaSPAdes) and predicted peptides (ending in .pep; predicted with
 TransDecoder). Both in fasta-format. 2. Mitochondrial cytochrome c oxidase
 (COI) sequences of invertebrate hosts ('2-host-COIs.fasta', in
 fasta-format). 3. SSU rRNA gene alignment of gregarines and other
 apicomplexans. Unmasked (aligned with MAFFT, ending in .muscle.fasta) and
 trimmed alignment files (trimmed with gblocks, ending in .gblocks.fasta;
 both in fasta-format), and corresponding treefile (RAxML-ng with 1,000
 bootstraps under GTR+Gamma model; ending in .tre, NEWICK-format). 4.
 Multigene single-gene data. This includes the folders: *
 'mafft': 263 single-gene alignments (all in fasta-format),
 aligned with MAFFT L-INS-I * 'bmge': 263 single-gene trimmed
 alignments (all in fasta-format), trimmed with BMGE * 'SGTs':
 263 single-gene treefiles (all in NEWICK-format), estimated with IQTree
 under the LG4X model and 1,000 ultrafast bootstraps 5. Multigene
 concatenated data. This includes the folders: * 'main_190gene':
 multigene concatenation alignment of 63 apicomplexan taxa and 190 genes
 (concatenation_190gene_over40per.Jul2-2023.sani.fasta; in fasta-format)
 and corresponding treefiles derived from phylogenetic analysis, generated
 with IQTree2 under the LG+C60+F+G model with 1,000 Ultrafast Bootstraps
 (file 'concatenation_190gene_UFB.treefile') and 200
 non-parametric boostraps under the PMSF model (file
 'concatenation_190gene_PMSF.treefile'). Both treefiles are in
 NEWICK-format. * '129gene': multigene concatenation of 63 taxa
 and 129 genes (CAT_63S129F.fasta; in fasta-format), and corresponding
 treefile estimated with IQTree2 under the LG+C60+F+G model with 1,000
 Ultrafast Bootstraps (CAT_63S129F.fasta.treefile; in NEWICK-format). *
 '22gene': multigene concatenation of 63 taxa and 129 genes
 (CAT_63S22F.fasta; in fasta-format), and corresponding treefile estimated
 with IQTree2 under the LG+C60+F+G model with 1,000 Ultrafast Bootstraps
 (CAT_63S22F.fasta.treefile; in NEWICK-format). *
 'fast-site_removal': 12 fasta-format alignment files ending in
 .fas, 12 treefiles generated with running the corresponding alignment file
 in IQTree2 under LG+C20+F+G and 1,000 Ultrafast Bootstraps. The alignment
 files were generated by using PhyloFisher's fast_site_remover.py
 script
 ([https://github.com/TheBrownLab/PhyloFisher](https://github.com/TheBrownLab/PhyloFisher) ) to remove 3,000 fast-evolving amino acid sites at each step. * 'heterotacheous-site_removal': 12 fasta-format alignment files ending in .fas, 12 treefiles generated with running the corresponding alignment file in IQTree2 under LG+C20+F+G and 1,000 Ultrafast Bootstraps. The alignment files were generated by using PhyloFisher's heterotachy.py script ([https://github.com/TheBrownLab/PhyloFisher](https://github.com/TheBrownLab/PhyloFisher) ) to remove 3,000 heterotacheous amino acid sites at each step * 'SR4_aa-recoding': one alignment file in fasta-format and corresponding treefile generated with IQTree2 under the GTR+R6+F model and 1,000 Ultrafast Bootstraps. To generate this alignment, the original alignment from 'main_190gene' was recoded to SR4 using PhyloFisher's recoder.py script ([https://github.com/TheBrownLab/PhyloFisher](https://github.com/TheBrownLab/PhyloFisher) ) with the -re SR4 option. 6. Raw images. In JPEG or RAW-format (ending in .ARW). This includes individual folders for each taxon: * Devanium_cincinnus_Ph216 * Devanium_robustum_SelFal * Lunidium_laculatum_SNEK * Lunidium_proboscidis_SNEKD * Lunidium_shako_KNOB * Metzidium_perlucensae_SQU2901 * Selenidium_capillus_Ph213 * Selenidium_natalis_SEL2980 * Selenidium_pherusae_Ph226 * Siedleckia_nematoides_BL3 ## Sharing/Access information Raw Illumina read data is deposited under NCBI BioProject accession PRJNA1090553, and SSU rDNA sequences of all reported taxa can be found under NCBI accessions PP553612 to PP553623.