The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

Abstract

Background: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. Results: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.

Comparing Early Eukaryotic Integration of Mitochondria and Chloroplasts in the Light of Internal ROS Challenges: Timing is of the Essence

“…This process was completed in LECA for all universally conserved supernumerary proteins (ϳ75 novel subunits). This conclusion is borne out by the reconstructed mitoproteome (from a draft nuclear genome sequence) of the jakobid Andalucia godoyi (47). Jakobids, which have the largest mitochondrial genomes known so far (48), though displaying a few ancient (bacterial) mitochondrial features, thus cannot be seen as "transitional" (47).…”

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

“…Tools such as MAKER [42][43][44][45] and PASA [36] closely depend on pre-assembled full-length transcripts to generate annotations. ESTs and/or de novo assembled transcriptomes have been often provided as inputs to these tools to generate annotations [46][47][48][49][50][51][52]. Transcripts constructed via de novo [53][54][55][56][57] or genomeguided [58][59][60][61][62][63] approaches are sensitive to the nature of the assembler and its parameter settings.…”

An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome

“…2018 ). More importantly, LECA’s mitoribosome has apparently recruited numerous novel proteins—here referred to as mitochondrion-specific mitoribosomal proteins (M-mtRPs)—whose most recent count has been established at 18 ( Gray et al. 2020 ).…”

“…2014 ). Indeed, our recent in silico mitoproteome analysis of Andalucia characterizes this species as “the eukaryote whose mitochondrion likely resembles the LECA mitochondrion more closely than does the mitochondrion in any other eukaryote studied to date” ( Gray et al. 2020 ).…”

“…Our previous in silico analyses predicted that the Andalucia mitoribosome includes as many as 70 mtRPs. Of these, 28 were predicted to be associated with the SSU and 42 with the LSU, of which 12 and 16, respectively, are mtDNA-encoded ( Gray et al. 2020 ).…”