The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?

Lima, Nicholas Costa Barroso; Prosdocimi, Francisco

doi:10.1080/24701394.2016.1275603

Cited by 16 publications

(10 citation statements)

References 26 publications

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“…As in other molluscs, with the exception of some bivalves 21 , M. neritoides transcribes its mitogenome on two strands, with all genes, except eight tRNAs, being encoded on the plus strand. The plus strand in M. neritoides corresponds to the heavy strand, which is originally defined as the strand with the higher amount of G + T nucleotides, although often mistakenly assigned as the strand encoding the majority of genes 28 . There are five overlapping adjacent genes in M. neritoides [ rrnS and trnV(tac) , trnV(tac) and rrnL , rrnL and trnL2(taa) , nad4l and nad4 , nad5 and trnF(gaa) ] versus six in Littorina sp.…”

Section: Resultsmentioning

confidence: 99%

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Fourdrilis

Martins

Backeljau

2018

Sci Rep

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Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.

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Section: Resultsmentioning

confidence: 99%

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Fourdrilis

Martins

Backeljau

2018

Sci Rep

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“…Therefore, the authors applied different procedures to determine the plus strand: it is likely that the first group selected the strand with the cox1 gene as the plus strand, whereas the second group selected the strand with more genes than the plus strand. This specific annotation issue has already been discussed [ 177 ]. Once again, we underline the necessity to determine and adopt conventions for the annotation of mitogenomes.…”

Section: Conclusion and Final Remarksmentioning

confidence: 99%

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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“…PhyloSuite [64] was used to parse and extract mitogenomes annotated in Microsoft Word documents, as well as to create the files for submission to GenBank and generate comparative mitogenomic architecture tables. Following the arguments put forward before [65], instead of referring to strands as heavy and light, we used plus (+) and minus (−) to denominate the strands encoding a majority and minority of genes, respectively. The mitogenomes are available from the GenBank repository under the accession numbers MK354235 (GL) and MK354236 (GP).…”

Section: Sequence Assembly and Analysismentioning

confidence: 99%

Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris

Sun

et al. 2020

R. Soc. open sci.

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We hypothesized that the mitogenome of Gammarus lacustris (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of Gammarus pisinnus (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% atp8 to 76.1% cox1 ). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and Gammarus fossarum exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in atp8 ) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining Gammarus species populating the same geographical range as GP.

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The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?

Cited by 16 publications

References 26 publications

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

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

Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris

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