ArticleFrontiers in plant science2023
Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction.
Article in Frontiers in plant science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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102 citing papers in PubMed.
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- An ancestral mitochondrial DNA insertion disrupts RNAi and enables persistence of a novel mycovirus inbioRxiv : the preprint server for biology · 2026Article
- Insights into the Phylogeny and Enigmatic Mitochondrial Biology of Eustigmatophyte Algae From Over 50 Newly Sequenced Organellar Genomes.Genome biology and evolution · 2026Article
- Mitochondrial Genome Reduction and Accelerated Evolution in Planktonic Foraminiferans.MicrobiologyOpen · 2026Article
- The complete mitochondrial genome data of the native, undescribedData in brief · 2026Article
- Complete plastid and mitochondrial genomes of the coralline marine red algaeMicrobiology resource announcements · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of the endangered plant Fraxinus mandshurica.BMC plant biology · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of Polygonatum odoratum (Yuzhu), a medicine-food homologous plant.BMC plant biology · 2026Article
- Chromosome-level de novo assembly of the nuclear and mitochondrial genomes of Arcopilus aureus, a filamentous fungus with multifaceted ecological and economic roles.Scientific data · 2026Article
- First telomere-to-telomere gapless genome assembly of the blackleg fungus Plenodomus lingam.Scientific data · 2026Article
- RhoMitoAnnotator and Polypods, Bioinformatics Tools for theInternational journal of molecular sciences · 2026Article
- Nucleo-cytoplasmic compatibility in interspecies Saccharomyces hybrids and the destabilisation of the mitogenome by allospecific recombination.Scientific reports · 2026Article
- Recurrent Modular Assembly Drives Independent Origins of Group II Introns Encoding LAGLIDADG Homing Endonucleases.Genome biology and evolution · 2026Article
- Comparative mitochondrial genome analyses of five medicinal mushroom Sanghuangporus provide insights into conservation, variation, and phylogenetic relationships.BMC genomics · 2026Article
- Molecular and physiological acclimation to low light and iron scarcity in a globally abundant oceanic pelagophyte.Nature communications · 2026Article
- Article
- Mitochondrial Graph-Based Pan-Genome Analysis ofInternational journal of molecular sciences · 2026Article
- Phylogenetic Relationships of Five Phallales Species Based on Mitochondrial Genome Analysis.Journal of fungi (Basel, Switzerland) · 2026Article
- Structural Remodeling and Enzymatic Replacement Shape the Evolution of Organellar Group II Introns inInternational journal of molecular sciences · 2026Article
- Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages.Genome biology and evolution · 2026Article
42 more citing papers are in PubMed but not listed here.
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts. The most difficult steps are (i) the structural modelling of intron-containing genes; (ii) the identification and delineation of Group I and II introns; and (iii) the identification of moderately conserved, non-coding RNA (ncRNA) genes specifying 5S rRNAs, tmRNAs and RNase P RNAs. Additional challenges arise through genetic code evolution which can redefine the translational identity of both start and stop codons, thus obscuring protein-coding genes. Further, RNA editing can render gene identification difficult, if not impossible, without additional RNA sequence data. Current automated mito- and plastid-genome annotators are limited as they are typically tailored to specific eukaryotic groups. The MFannot annotator we developed is unique in its applicability to a broad taxonomic scope, its accuracy in gene model inference, and its capabilities in intron identification and classification. The pipeline leverages curated profile Hidden Markov Models (HMMs), covariance (CMs) and ERPIN models to better capture evolutionarily conserved signatures in the primary sequence (HMMs and CMs) as well as secondary structure (CMs and ERPIN). Here we formally describe MFannot, which has been available as a web-accessible service (https://megasun.bch.umontreal.ca/apps/mfannot/) to the research community for nearly 16 years. Further, we report its performance on particularly intron-rich mitogenomes and describe ongoing and future developments.
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