Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.

Summary Iron (Fe) is essential for virtually all organisms, being irreplaceable because of its electrochemical properties that enable many biochemical processes, including photosynthesis. Besides its abundance, Fe is generally found in the poorly soluble form of ferric iron (Fe3+), while most plants uptake the soluble form Fe2+. The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers rhizosphere pH through proton pumping that increases Fe3+ solubility, which is then reduced by a membrane‐bound reductase and transported into the cell by the zinc‐regulated, iron‐regulated transporter‐like protein (ZIP) family protein AtIRT1. ZIP proteins are transmembrane transporters of divalent metals such as Fe2+, Zn2+, Mn2+, and Cd2+. In this work, we investigated the evolution of functional homologs of IRON‐REGULATED TRANSPORTER 1/ZIP in the supergroup Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using 51 genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe2+ uptake by ZIP proteins evolved independently at least twice throughout green plant evolution. Our results indicate that the archetypical IRON‐REGULATED TRANSPORTER (IRT) proteins from angiosperms likely emerged before the origin of land plants during early streptophyte algae terrestrialization, a process that required the evolution of Fe acquisition in terrestrial subaerial settings.

Iron (Fe) is an essential micronutrient for virtually all living beings, being practically irreplaceable because of its unique electrochemical properties that enable or facilitate a series of biochemical processes, including photosynthesis. Although Fe is abundant on Earth, it is generally found in the poorly soluble form Fe3+. Most extant plants have established Fe absorption strategies that involve Fe uptake in the soluble form Fe2+. The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers the pH through proton pumping to the rhizosphere to increase Fe3+ solubility, which is then reduced by a plasma membrane-bound reductase and transported into the cell by the ZIP family protein IRT1. ZIP proteins are transmembrane transporters of a variety of divalent metals such as Fe2+, Zn2+, Mn2+ and Cd2+. In this work, we investigate the evolution of functional homologs of IRT1/ZIP in the supergroup of photosynthetic eukaryotes Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using a dataset of 41 high-quality genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe2+ uptake by ZIP family proteins evolved at least twice independently during green plant evolution. Sequence and structural analyses indicate that the archetypical IRT proteins from angiosperms likely emerged in streptophyte algae before the origin of land plants and might be an important player in green plant terrestrialization, a process that involved the evolution of Fe acquisition in terrestrial subaerial settings.

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