HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades

Plazzi, Federico; Puccio, Guglielmo; Passamonti, Marco

doi:10.1016/j.mito.2021.02.009

Cited by 2 publications

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References 153 publications

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“…A customized version of the HERMES tool [ 137 ] was used to analyze the dataset. The method involves the computation of several variables from annotated complete mitochondrial genomes.…”

Section: Methodsmentioning

confidence: 99%

“…These metrics are usually summarized in a single number, the HERMES index, by means of a maximum likelihood factor analysis. For the present purpose, though, the HERMES index itself and variables stemming from a phylogenetic tree—such as AMIGA [ 137 ], root-to-tip distance, and maximum likelihood distance)—which were obviously not available in this context, were excluded. The following 11 variables are, therefore, considered and computed for each entry: length of the mtDNA, topology (linear or circular), number of annotated genes, absolute value of the Strand Usage skew (SU-skew; see [ 137 ] for definition), A+T content, AT-skew, GC-skew, CAI, percentage of Unassigned Regions (URs), UR-based A+T content, and UR-based median length.…”

Section: Methodsmentioning

confidence: 99%

“…In the present paper, we obtained from GenBank all the available complete mitochondrial genomes and used a slightly modified version of a recently published tool [ 137 ] to analyze the dataset. Exactly 40 years after the first complete mitochondrial sequence, we present a general description of our results; we also identify mitochondrial features typical of different taxa, aiming to provide a global overview of mitochondrial molecular diversity.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Formaggioni

Luchetti

Plazzi

2021

Life

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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.

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“…A customized version of the HERMES tool [ 137 ] was used to analyze the dataset. The method involves the computation of several variables from annotated complete mitochondrial genomes.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

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Luchetti

Plazzi

2021

Life

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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks

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Plazzi

Passamonti

2022

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Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.

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HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades

Cited by 2 publications

References 153 publications

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

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

Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks

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