Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean<i>Armadillidium vulgare</i>

Doublet, Vincent; Ubrig, Élodie; Alioua, Abdelmalek; Bouchon, Didier; Marcadé, Isabelle; Maréchal-Drouard, Laurence

doi:10.1080/15476286.2015.1090078

Cited by 37 publications

(53 citation statements)

References 53 publications

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“…The longest two overlaps are between trnW / trnC and ND4L / trnT genes (Table 1). Overlapping genes might be a refl ection of the selection for a short and economic mitogenome, and they usually involve trn genes, because their sequences are constrained by fewer mutations (Doublet et al, 2015).…”

Section: Intergenic Spacers Overlapping Sequences and The At-rich Rementioning

confidence: 99%

Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Liu¹,

Li²,

Jakovlić³

et al. 2017

Eur. J. Entomol.

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Section: Intergenic Spacers Overlapping Sequences and The At-rich Rementioning

confidence: 99%

Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Liu¹,

Li²,

Jakovlić³

et al. 2017

Eur. J. Entomol.

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“…Furthermore, isopod mitogenomes generally exhibit a large number of gene order rearrangements [4,11], and some groups of isopods even possess a non-standard, linearised, mitogenome organisation and unique tRNA-encoding mechanisms [12–16]. As the evolution of mitogenomic architecture appears to be highly discontinuous [17,18], with some major animal taxa exhibiting a highly conserved mitochondrial architecture (most vertebrates being a good example), and other taxa exhibiting a rapidly-evolving architecture [17–21], we hypothesise that isopods might present an important model system to study the complex dynamics of the evolution of mitochondrial genomic architecture.…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

et al. 2018

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As a result of great diversity in life histories and a large number of described species, taxonomic and phylogenetic uncertainty permeates the entire crustacean order of Isopoda. Large molecular datasets capable of providing sufficiently high phylogenetic resolution, such as mitochondrial genomes (mitogenomes), are needed to infer their evolutionary history with confidence, but isopod mitogenomes remain remarkably poorly represented in public databases. We sequenced the complete mitogenome of Cymothoa indica, a species belonging to a family from which no mitochondrial genome was sequenced yet, Cymothoidae. The mitogenome (circular, 14484 bp, A+T = 63.8%) is highly compact, appears to be missing two tRNA genes (trnI and trnE), and exhibits a unique gene order with a large number of rearrangements. High compactness and the existence of palindromes indicate that the mechanism behind these rearrangements might be associated with linearization events in its evolutionary history, similar to those proposed for isopods from the Armadillidium genus (Oniscidea). Isopods might present an important model system to study the proposed discontinuity in the dynamics of mitochondrial genomic architecture evolution. Phylogenetic analyses (Bayesian Inference and Maximum Likelihood) conducted using nucleotide sequences of all mitochondrial genes resolved Oniscidea and Cymothoida suborders as paraphyletic. Cymothoa indica was resolved as a sister group (basal) to all remaining isopods, which challenges the accepted isopod phylogeny, where Cymothoida are the most derived, and Phreatoicidea the most basal isopod group. There is growing evidence that Cymothoida suborder might be split into two evolutionary distant clades, with parasitic species being the most basal split in the Isopoda clade, but a much larger amount of molecular resources carrying a high phylogenetic resolution will be needed to infer the remarkably complex evolutionary history of this group of animals with confidence.

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“…It is notable for its compaction. In particular, genes coding transfer RNAs (tRNAs) can partially or fully overlap with protein coding genes (Doublet et al 2015). But one truly unique feature of this genome is the capacity of three tRNA loci to each encode two alternative tRNAs with distinct anticodons, thanks to single nucleotide polymorphisms (SNPs) occurring within the same individual (Marcadé et al 2007;Doublet et al 2008;Chandler et al 2015).…”

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confidence: 99%

Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing

et al. 2017

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The highly compact mitochondrial (mt) genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ∼14 kb linear monomer and a ∼28 kb circular dimer comprising two monomer units fused in palindrome. We hypothesized that heteroplasmy actually results from two genome units of the same dimeric molecule carrying different tRNA genes at mirrored loci. This hypothesis, however, contradicts the earlier proposition that dimeric molecules result from the replication of linear monomers-a process that should yield totally identical genome units within a dimer. To solve this contradiction, we used the SMRT (PacBio) technology to sequence mirrored tRNA loci in single dimeric molecules. We show that dimers do present different tRNA genes at mirrored loci; thus covalent linkage, rather than balancing selection, maintains vital variation at anticodons. We also leveraged unique features of the SMRT technology to detect linear monomers closed by hairpins and carrying noncomplementary bases at anticodons. These molecules contain the necessary information to encode two tRNAs at the same locus, and suggest new mechanisms of transition between linear and circular mtDNA. Overall, our analyses clarify the evolution of an atypical mt genome where dimerization counterintuitively enabled further mtDNA compaction.

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Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustaceanArmadillidium vulgare

Cited by 37 publications

References 53 publications

Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing

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