Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features

Kutyumov, Vladimir A.; Predeus, Alexander V.; Starunov, Viktor V.; Maltseva, Arina L.; Ostrovsky, Andrew N.

doi:10.1016/j.mito.2021.02.003

Cited by 3 publications

(5 citation statements)

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“…A handful of tRNAs have been identified in cnidarians (e.g., [78,123]), where additional genes are present ( [124] and references therein); similarly, many genes that are usually found in animal mtDNA are missing from that of ctenophores (tRNAs, atp6, atp8; [79,81,116,125]). This summary of mitochondrial molecular structures and architectures certainly gives an idea of the stunning variability of these organellar genomes, which largely surpasses that of plastid trans-splicing phenomena [19,78,81,126]; the use of different genetic codes [13,127,128]; bewildering gene rearrangement [81][82][83][84][85][86][87][88]105,106,[129][130][131]; and biparental and doubly uniparental inheritance [28,30,58,[132][133][134][135][136].…”

Section: Introductionmentioning

confidence: 99%

“…This summary of mitochondrial molecular structures and architectures certainly gives an idea of the stunning variability of these organellar genomes, which largely surpasses that of plastid trans-splicing phenomena [ 19 , 78 , 81 , 126 ]; the use of different genetic codes [ 13 , 127 , 128 ]; bewildering gene rearrangement [ 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 105 , 106 , 129 , 130 , 131 ]; and biparental and doubly uniparental inheritance [ 28 , 30 , 58 , 132 , 133 , 134 , 135 , 136 ].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

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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“…Using nucleotide sequences and gene arrangement information from protein‐coding and rRNA genes, we examined the evolutionary relationships between H. destructor and other Trombidiformes with complete mitogenomes (for genetic maps, see Appendix: Figures S1–S7 ). Gene arrangements can provide alternative characters to track evolutionary relationships among different taxa (Froufe et al., 2020 ; Gong et al., 2019 ; Inoue et al., 2003 ; Kutyumov et al., 2021 ). Prior analyses of mitogenomic structural haplotypes in trombidiform mites have focused on a comparatively smaller number of species to that analyzed in our study (Edwards et al., 2011 ; Li & Xue, 2019 ; Palopoli et al., 2014 ; Shao et al., 2005 ; Xue et al., 2017 ; Xue et al., 2016 ).…”

Section: Resultsmentioning

confidence: 99%

“…In particular, complete mitochondrial sequences could provide greater capacity to resolve taxonomy among members of the Trombidiformes, given the unusually high incidence of mitogenomic rearrangements that have occurred in this order that complicate phylogenetic analyses of sequence data from single genes (Edwards et al., 2011 ; Palopoli et al., 2014 ; Shao et al., 2005 ). Structural haplotypes in mitochondrial gene arrangements have provided insights into evolutionary relationships across diverse taxa (Froufe et al., 2020 ; Gong et al., 2019 ; Inoue et al., 2003 ; Kutyumov et al., 2021 ), but to date, such analyses have been relatively small in scope with respect to the Trombidiformes, typically focusing on a few species (Edwards et al., 2011 ; Li & Xue, 2019 ; Palopoli et al., 2014 ; Shao et al., 2005 ; Xue et al., 2017 ; Xue et al., 2016 ).…”

Section: Introductionmentioning

confidence: 99%

The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements

Thia

Young

Korhnen

et al. 2021

Ecology and Evolution

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The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein-coding genes, two rRNA genes, and 22 tRNA genes.We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein-coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co-occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro-ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.

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“…However, recent research has shown that this may not always be the case, challenging the notion of ubiquitous features in metazoan mitochondrial genomics (Lavrov et al 2013;Breton et al 2014;Formaggioni et al 2021). Actually, animal mitochondrial genomes are highly variable for what concerns genome architecture (Lavrov and Pett 2016); genome size (Pu et al 2019;Hemmi et al 2020); use of different genetic codes (Lavrov et al 2013;Li et al 2018); gene arrangement (Trindade Rosa et al 2017;Pu et al 2019;Hemmi et al 2020;Monnens et al 2020;Ghiselli et al 2021;Kutyumov et al 2021); doubly uniparental inheritance (DUI; Passamonti and Ghiselli 2009;Zouros and Rodakis 2019;; and post-transcriptional regulation (Osigus et al 2017;Schuster et al 2017).…”

Section: Mitochondrial Secondary Structures Are Easily Co-opted To De...mentioning

confidence: 99%

Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

Plazzi,

Le Cras,

Formaggioni

et al. 2023

Heredity

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Several functional classes of short noncoding RNAs are involved in manifold regulatory processes in eukaryotes, including, among the best characterized, miRNAs. One of the most intriguing regulatory networks in the eukaryotic cell is the mito-nuclear crosstalk: recently, miRNA-like elements of mitochondrial origin, called smithRNAs, were detected in a bivalve species, Ruditapes philippinarum. These RNA molecules originate in the organelle but were shown in vivo to regulate nuclear genes. Since miRNA genes evolve easily de novo with respect to protein-coding genes, in the present work we estimate the probability with which a newly arisen smithRNA finds a suitable target in the nuclear transcriptome. Simulations with transcriptomes of 12 bivalve species suggest that this probability is high and not species specific: one in a hundred million (1 × 10 −8 ) if five mismatches between the smithRNA and the 3' mRNA are allowed, yet many more are allowed in animals. We propose that novel smithRNAs may easily evolve as exaptation of the pre-existing mitochondrial RNAs. In turn, the ability of evolving novel smithRNAs may have played a pivotal role in mito-nuclear interactions during animal evolution, including the intriguing possibility of acting as speciation trigger.

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Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features

Cited by 3 publications

References 73 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

The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements

Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

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