Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence

Abstract

Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.

Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements

“…These uORF elements have been identified in different fungal mitogenomes, and some may be shared among species, as recently demonstrated ( Fonseca et al, 2020 ; Araújo et al, 2021 ; Kulik et al, 2021 ), which suggests that uORFs within mitogenomes of fungi may play a significant role in shaping mitochondrial genome length. This is in agreement with a recent investigation of mitochondrial landscape in eukaryotes, which has found a positive correlation between mitochondrial genome length and the prevalence of unassigned regions ( Formaggioni et al, 2021 ). Nonetheless, differences in the literature suggest that there are probably inter-phyla variations.…”

“…Mitochondrial plasmids are widely found in Fungi and some mitochondrial genes, such as dpo and rpo , are commonly associated with plasmid integration events ( Formighieri et al, 2008 ; Férandon et al, 2013 ; Formaggioni et al, 2021 ). In our study, we identified dpo homologs in at least one species of six different phyla, with Basidiomycota and Ascomycota showing the highest numbers of sequences – 227 and 116, respectively ( Supplementary Table 5 ).…”

“…In fungi, mitogenomes can be linear or circular. Circular mitogenomes are by far the most common, while linear mitogenomes are mainly described in yeasts, such as Saccharomyces cerevisiae (Ascomycota) ( Williamson, 2002 ; Formaggioni et al, 2021 ). Typical fungal mitogenomes such as those belonging to Ascomycota and Basidiomycota (Dikarya Subkingdom) usually display a core genome with 14 conserved protein-coding genes ( atp6 , 8 , and 9; cob ; cox1– 3; and nad1– 6, 4L ), the ribosomal genes rnl and rns , and from 20 and 31 tRNA genes ( Zardoya, 2020 ; Kulik et al, 2021 ).…”

“…Typical fungal mitogenomes such as those belonging to Ascomycota and Basidiomycota (Dikarya Subkingdom) usually display a core genome with 14 conserved protein-coding genes ( atp6 , 8 , and 9; cob ; cox1– 3; and nad1– 6, 4L ), the ribosomal genes rnl and rns , and from 20 and 31 tRNA genes ( Zardoya, 2020 ; Kulik et al, 2021 ). The genomes belonging to subkingdom Dikarya also have the ribosomal protein gene rps3 that is lacking in some taxa, such as the genus Candida ( Freel et al, 2015 ; Formaggioni et al, 2021 ). Mitogenome length is also quite variable among fungal taxa, ranging from 12 to 272 kbp in Rozella allomycis and Morchella crassipes , respectively ( James et al, 2013 ; Liu et al, 2020 ).…”

Molecular Phylogenetics and Mitochondrial Evolution

“…The present Special Issue is an attempt to set and assess the state-of-art of mitochondrial genomics, with special reference to the suitability of mtDNAs for phylogenetic inference. The work by Formaggioni and colleagues [6] opens the Special Issue with a broad-scale analysis of the current knowledge on mitochondrial genomics, presenting the largest-to-date database of mtDNA features, which was made freely available to the scientific community. Similarly, the review by Parakatselaki and Ladoukakis [7], which closes the Special Issue, is specifically focused on mitochondrial heteroplasmy, a well-known phenomenon which is in fact neglected among the dogmatic "widespread" features of mitochondrial genomics, which include the strict maternal inheritance.…”