The complete mitochondrial genome of Paravannella minima (Amoebozoa, Discosea, Vannellida)

Bondarenko, Natalya; Glotova, Anna; Nassonova, Elena; Masharsky, Alexey; Polev, Dmitry E.; Smirnov, Alexey V.

doi:10.1016/j.ejop.2019.01.005

Cited by 6 publications

(12 citation statements)

References 32 publications

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“…This is consistent with the high percentage of A + T content in the nucleotide composition of PCGs as well as in other mt genomes of Amoebozoa (Bondarenko et al. ,b,c, ; Burger et al. ; Greninger et al.…”

Section: Resultssupporting

confidence: 83%

“…However, they both are significantly shorter than the mt genome of another vannellid ameba, Paravannella minima , which has the size of 53.4 kbp (Bondarenko et al. ). If we look “down” to the phylogenetic tree, the outgroup to the clade unifying vannellids and dactylopodids is Centramoebida.…”

Section: Resultsmentioning

confidence: 99%

“…Mitochondrial genome analysis is a powerful instrument for evolutionary studies, and the dataset on the mitochondrial genomes of amebae is slowly growing in taxonomic coverage (Bondarenko et al. ,b,c, ; Fučikova and Lahr ; Greninger et al. ; Pombert et al.…”

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confidence: 99%

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A Comparative Characterization of the Mitochondrial Genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae)

Bondarenko

Volkova

Masharsky

et al. 2019

J Eukaryotic Microbiology

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Marine amebae of the genus Paramoeba (Amoebozoa, Dactylopodida) normally contain a eukaryotic endosymbiont known as Perkinsela‐like organism (PLO). This is one of the characters to distinguish the genera Neoparamoeba and Paramoeba from other Dactylopodida. It is known that the PLO may be lost, but PLO‐free strains of paramoebians were never available for molecular studies. Recently, we have described the first species of the genus Paramoeba which has no parasome—Paramoeba aparasomata. In this study, we present a mitochondrial genome of this species, compare it with that of Neoparamoeba pemaquidensis, and analyze the evolutionary dynamics of gene sequences and gene order rearrangements between these species. The mitochondrial genome of P. aparasomata is 46,254 bp long and contains a set of 31 protein‐coding genes, 19 tRNAs, two rRNA genes, and 7 open reading frames. Our results suggest that these two mitochondrial genomes within the genus Paramoeba have rather similar organization and gene order, base composition, codon usage, the composition and structure of noncoding, and overlapping regions.

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Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

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A Comparative Characterization of the Mitochondrial Genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae)

Bondarenko

Volkova

Masharsky

et al. 2019

J Eukaryotic Microbiology

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“…Within Amoebozoa, the mitogenomes of Conosea 110 and Lobosea 111 have similar sizes of 29 to 58 Kb (Figure 2). These circular mitogenomes generally have a core set of 19 OXPHOS subunit protein-coding genes (nad1-7, 9, 11, 4L; cob; cox1-3; atp1, 4, 6, 8, and 9) and several rps and rpl genes and unassigned ORFs [110][111][112] , although different species may have lost variously some of these genes; an extreme case is that of the free-living lobosean Vannella croatica, which lacks the nad3, 7, and 9; atp1, 4, 6, and 8; and all rps and rpl genes 113 . The rrnS and rrnL genes and 13 to 25 trn genes are present [110][111][112] .…”

Section: Other Eukaryote Mitogenome Structuresmentioning

confidence: 99%

Recent advances in understanding mitochondrial genome diversity

Zardoya

2020

F1000Res

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Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.

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“…Other strain designations are the author's ones (according to GenBank data). (Bondarenko et al, 2018b), Clydonella sawyery (Bondarenko et al, 2018c) and Paravannella minima (Bondarenko et al, 2019a). Among them the mt genome of Vannella croatica was obtained into two steps: the purified mitochondrial DNA that was isolated by pulsed-field gel electrophoresis was sequenced using NGS.…”

Section: Available Mitochondrial Genomes In Amoebozoamentioning

confidence: 99%

Mitochondrial genomes of Amoebozoa

Bondarenko¹,

Smirnov²,

Nassonova³

et al. 2019

Protistology

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In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial genomes as a promising tool for understanding evolutionary patterns in Amoebozoa.

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The complete mitochondrial genome of Paravannella minima (Amoebozoa, Discosea, Vannellida)

Cited by 6 publications

References 32 publications

A Comparative Characterization of the Mitochondrial Genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae)

A Comparative Characterization of the Mitochondrial Genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae)

Recent advances in understanding mitochondrial genome diversity

Mitochondrial genomes of Amoebozoa

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