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Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4939-7804-5_15openalex-snapshot

Fungal Genome Annotation

inferredcites →https://doi.org/10.1007/s002390010220openalex-snapshot

How Mitochondria Redefine the Code

inferredcites →https://doi.org/10.1007/s002940050220openalex-snapshot

The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression

inferredcites →https://doi.org/10.1007/s002940050234openalex-snapshot

Mitochondrial ATP synthase subunit 9 is not required for viability of the petite-negative yeast Kluyveromyces lactis

inferredcites →https://doi.org/10.1016/j.angen.2023.200161openalex-snapshot

Does Atp8 Exist in the Mitochondrial Genome of Proseriata (Metazoa: Platyhelminthes)?

inferredcites →https://doi.org/10.1016/j.cell.2012.02.035openalex-snapshot

Mitochondria: In Sickness and in Health

inferredcites →https://doi.org/10.1016/j.cub.2013.06.057openalex-snapshot

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

inferredcites →https://doi.org/10.1016/j.cub.2016.03.053openalex-snapshot

A Eukaryote without a Mitochondrial Organelle

inferredcites →https://doi.org/10.1016/j.cub.2017.03.075openalex-snapshot

Marine Protists Are Not Just Big Bacteria

inferredcites →https://doi.org/10.1016/j.cub.2017.09.015openalex-snapshot

The Origin and Diversification of Mitochondria

inferredcites →https://doi.org/10.1016/j.funeco.2023.101274openalex-snapshot

ITS alchemy: On the use of ITS as a DNA marker in fungal ecology

inferredcites →https://doi.org/10.1016/j.funeco.2024.101383openalex-snapshot

Fungal diversity and function in metagenomes sequenced from extreme environments

inferredcites →https://doi.org/10.1016/j.margen.2010.01.001openalex-snapshot

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): Identification of the “missing” ATPase 8 gene

inferredcites →https://doi.org/10.1016/j.ympev.2012.08.023openalex-snapshot

MITOS: Improved de novo metazoan mitochondrial genome annotation

inferredcites →https://doi.org/10.1016/j.ympev.2018.04.037openalex-snapshot

Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes

inferredcites →https://doi.org/10.1038/nature12985openalex-snapshot

Mitochondrial form and function

inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

inferredcites →https://doi.org/10.1038/s41559-021-01638-2openalex-snapshot

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria

inferredcites →https://doi.org/10.1038/s41576-018-0035-9openalex-snapshot

Cytonuclear integration and co-evolution

inferredcites →https://doi.org/10.1038/s41598-018-25759-0openalex-snapshot

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

inferredcites →https://doi.org/10.1038/s41598-022-09512-2openalex-snapshot

Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

inferredcites →https://doi.org/10.1073/pnas.1410442111openalex-snapshot

Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

inferredcites →https://doi.org/10.1073/pnas.1604560113openalex-snapshot

Assembly of long error-prone reads using de Bruijn graphs

inferredcites →https://doi.org/10.1093/bioinformatics/bth352openalex-snapshot

Automatic annotation of organellar genomes with DOGMA

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btt509openalex-snapshot

Infernal 1.1: 100-fold faster RNA homology searches

inferredcites →https://doi.org/10.1093/femsyr/fov023openalex-snapshot

Mitochondrial genome evolution in yeasts: an all-encompassing view

inferredcites →https://doi.org/10.1093/g3journal/jkac285openalex-snapshot

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi

inferredcites →https://doi.org/10.1093/gbe/evaa126openalex-snapshot

The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG)

inferredcites →https://doi.org/10.1093/gbe/evu028openalex-snapshot

High Variability of Mitochondrial Gene Order among Fungi

inferredcites →https://doi.org/10.1093/icb/icz025openalex-snapshot

Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msp077openalex-snapshot

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

inferredcites →https://doi.org/10.1093/molbev/msr025openalex-snapshot

Two Nuclear Life Cycle-Regulated Genes Encode Interchangeable Subunits c of Mitochondrial ATP Synthase in Podospora anserina

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msx197openalex-snapshot

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

inferredcites →https://doi.org/10.1093/nar/25.3.626openalex-snapshot

Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine

inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

inferredcites →https://doi.org/10.1093/nar/gkaa1047openalex-snapshot

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

inferredcites →https://doi.org/10.1093/nar/gkaa913openalex-snapshot

Pfam: The protein families database in 2021

inferredcites →https://doi.org/10.1093/nar/gkac278openalex-snapshot

DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

inferredcites →https://doi.org/10.1093/nar/gkac976openalex-snapshot

The IMG/M data management and analysis system v.7: content updates and new features

inferredcites →https://doi.org/10.1093/nar/gkg264openalex-snapshot

Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gks1160openalex-snapshot

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

inferredcites →https://doi.org/10.1093/nar/gkt1183openalex-snapshot

MycoCosm portal: gearing up for 1000 fungal genomes

inferredcites →https://doi.org/10.1093/nar/gku1063openalex-snapshot

Rfam 12.0: updates to the RNA families database

inferredcites →https://doi.org/10.1093/nar/gkz173openalex-snapshot

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004084openalex-snapshot

Hyaloraphidium curvatum: A Linear Mitochondrial Genome, tRNA Editing, and an Evolutionary Link to Lower Fungi

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot

Circos: An information aesthetic for comparative genomics

inferredcites →https://doi.org/10.1111/j.1469-8137.2005.01492.xopenalex-snapshot

Inheritance and recombination of mitochondrial genomes in plants, fungi and animals

inferredcites →https://doi.org/10.1111/mec.13195openalex-snapshot

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

inferredcites →https://doi.org/10.1111/nyas.13222openalex-snapshot

Dissecting genome reduction and trait loss in insect endosymbionts

inferredcites →https://doi.org/10.1126/sciadv.abd0079openalex-snapshot

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

inferredcites →https://doi.org/10.1128/mbio.01676-23openalex-snapshot

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

inferredcites →https://doi.org/10.1137/040608635openalex-snapshot

Graph Clustering Via a Discrete Uncoupling Process

inferredcites →https://doi.org/10.1146/annurev-biochem-060109-092838openalex-snapshot

Mitochondrial tRNA Import and Its Consequences for Mitochondrial Translation

inferredcites →https://doi.org/10.1371/journal.pgen.1002876openalex-snapshot

Experimental Relocation of the Mitochondrial ATP9 Gene to the Nucleus Reveals Forces Underlying Mitochondrial Genome Evolution

inferredcites →https://doi.org/10.1371/journal.pgen.1008304openalex-snapshot

Variation and selection on codon usage bias across an entire subphylum

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0120081openalex-snapshot

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

inferredcites →https://doi.org/10.1534/g3.118.200948openalex-snapshot

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

inferredcites →https://doi.org/10.3389/fmicb.2014.00278openalex-snapshot

Parasites in algae mass culture

inferredcites →https://doi.org/10.3389/fmicb.2020.00765openalex-snapshot

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

inferredcites →https://doi.org/10.3389/fmicb.2021.647989openalex-snapshot

Pan-Mitogenomics Approach Discovers Diversity and Dynamism in the Prominent Brown Rot Fungal Pathogens

inferredcites →https://doi.org/10.3389/fmicb.2021.787283openalex-snapshot

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

inferredcites →https://doi.org/10.3389/fpls.2023.1222186openalex-snapshot

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction

inferredcites →https://doi.org/10.3390/ijms21020483openalex-snapshot

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

inferredcites →https://doi.org/10.7717/peerj.7359openalex-snapshot

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/mycokeys.140.205520zenodo-depositor-declared

Assembly and comparative analysis of the complete mitochondrial genomes of five Thaxterogaster species (Cortinariaceae, Basidiomycota): Insights into mitochondrial genome evolution and intrageneric phylogenetic relationships

inferred← citeshttps://doi.org/10.1016/j.fgb.2026.104104openalex-snapshot

An exceptionally large, intron-rich mitochondrial genome and complex RNA processing in the desert-dwelling fungus Helvella bachu

inferred← citeshttps://doi.org/10.1093/g3journal/jkag237openalex-snapshot

Genomic characterization of the endangered medicinal polypore agarikon ( Laricifomes officinalis syn. Fomitopsis officinalis )

inferred← citeshttps://doi.org/10.3390/jof12090648openalex-snapshot

The Complete Mitogenome of Alternaria brassicae Causing Black Spot Disease on Rapeseed-Mustard

inferred← citeshttps://doi.org/10.3390/jof12100729openalex-snapshot

Intron-Associated Mitogenome Size Variation and Gene-Specific Stop Codon Absence in the Lichen-Forming Genus Ramalina

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