DOI: 10.5061/dryad.73n5tb331
title: Data from: Extreme mitochondrial reduction in a novel group of free-living metamonads

description: Metamonads are a diverse group of heterotrophic microbial eukaryotes
 adapted to living in hypoxic environments. All metamonads but one harbour
 metabolically altered ‘mitochondrion-related organelles’ (MROs) with
 reduced functions, however the degree of reduction varies. Here, we
 generate high-quality draft genomes, transcriptomes, and predicted
 proteomes for five recently discovered free-living metamonads.
 Phylogenomic analyses placed these organisms in a group we name the ‘BaSk’
 (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the
 Fornicata, a phylum that includes parasitic and free-living flagellates.
 Bioinformatic analyses of gene models shows that these organisms are
 predicted to have extremely reduced MRO proteomes in comparison to other
 free-living metamonads. Loss of the mitochondrial iron-sulfur cluster
 assembly system in some organisms in this group appears to be linked to
 the acquisition in their common ancestral lineage of a SUF-like minimal
 system Fe/S cluster pathway through lateral gene transfer. One of the
 isolates, Skoliomonas litria, appears to have lost all other known MRO
 pathways. No proteins were confidently assigned to the predicted MRO
 proteome of this organism suggesting that the organelle has been lost. The
 extreme mitochondrial reduction observed within this free-living anaerobic
 protistan clade demonstrates that mitochondrial functions may be
 completely lost even in free-living organisms.
description: # README: Extreme mitochondrial reduction in a novel group of free-living
 metamonads --- Genomes, gene models, alignments, HMM profiles and
 supplementary datasets for the BaSk clade - *Skoliomonas litria*,
 *Skoliomonas* sp. GEMRC, *Skoliomonas* sp. RCL, and *Barthelona* sp. PCE.
 ## Description of the data and file structure **BaSk_clade_genome_genes**
 folder: * Genomes (.fsa) and gene models (.fasta and .gff3) for each
 species of the BaSk clade. **alignments_hmm** folder: *
 **alignments_hmm/phylogenomics -** final phylogenomic alignment along with
 a .txt file outline the presence/absence of each taxa for each
 concatenated gene. The .txt file also includes summary statistics for the
 number of present data (and % data presence) for each taxa and each gene.
 -  **alignments_hmm/MRO_protiens** - Alignments (.fas), corresponding HMM
 profiles, and raw phylogenetic trees relating to searches for MRO
 proteins, separated into folders according to similar biochemical pathways
 and functions. The **Anaerobic_metabolism** folder contains the
 corresponding files for proteins relating to ATP production, hydrogen
 production, and Fe-S cluster biogenesis. The **Chaperones** folder
 contains the corresponding files for cpn60 and hsp70. The **CIA** folder
 contains files for proteins of the CIA pathway. The **MRO_import** folder
 contains HMM profiles that were used to search for MRO membrane-bound
 transport proteins. The **SUFCB** folder contains the FAS and TREE files.
 **supplemental_data** folder: * Supp_Data_1_genes.xlsx - A spreadsheet
 that lists all gene mentioned in the manuscript (for each BaSk clade
 member). For each gene, the following information is listed: gene model
 number, nucleotide sequence, amino acid sequence, mitochondrial targeting
 prediction information from TargetP, MitoProt, and Mitofates, and
 expression level value (FPKM). Highlighted gene models have 2 or more
 targeting software that predicts that the protein is MRO localizing. In
 addition, there is a list of Fe-S cluster biogenesis proteins that were
 searched for as part of this study. * Supp_Data_2_HydA_PFO.xlsx - A
 spreadsheet listing HydA and PFO proteins in each BaSk clade member, the
 top BLAST hit to the NCBI nr database for each, along with notable protein
 domain fusions. * Supp_Data_3_FPKM.xlsx - A spreadsheet listing the top
 100 highly expressed gene models (in FPKM) for each BaSk clade member,
 annotated by top NCBI nr database hit. Highlighted gene models are
 proteins that are found in Supp_Data_1_genes.xlsx. * BaSk_FPKM.xlsx -
 Complete list of gene expression levels (FPKM) for all gene models in each
 BaSk clade member.