The complete mitochondrial genome of <i>Gruberia lanceolata</i> (Gruber, 1884) Kahl, 1932 (Ciliophora: Heterotrichea)

Park, Mi-Hyun; Min, Gi–Sik

doi:10.1080/23802359.2019.1674199

Cited by 4 publications

(2 citation statements)

References 17 publications

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“…In the years since those seminal discoveries, more ciliate mitogenomes have been characterized, including 20 mitogenomes from species in the class Oligohymenophorea ( Tetrahymena pyriformis , T. thermophila , T. malaccensis , T. paravorax , T. pigmentosa , T. rostrata , Ichthyophthirius multifiliis , Uronema marinum , Paramecium caudatum , P. aurelia , P. tetraurelia , P. sexaurelia , P. multimicronucleatum , P. biaurelia , P. octaurelia , P. novaurelia , P. decaurelia , P. dodecaurelia , P. quadecaurelia , and P. jenningsi ) [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ], eight mitogenomes of species in the class Spirotrichea ( Oxytricha trifallax , Laurentiella strenua , Stylonychia lemnae , Paraurostyla sp., Urostyla grandis , Pseudourostyla cristata , Euplotes minuta , and E. crassus ) [ 37 , 38 , 39 ], two mitogenomes in the class Heterotrichea ( Stentor coeruleus and Gruberia lanceolata ) [ 20 , 40 ], as well as seven hydrogenosomal genomes of anerobic ciliates ( Nyctotherus ovalis , Metopus contortus , Metopus es , Metopid sp., Heterometopus sp., Parablepharisma sp., and Muranothrix gubernata ) [ 41 , 42 , 43 ]. Ciliate mitogenomes are generally in size of 20–70 kb, with high A+T content (58.53% for N. ovalis ~81.51% for I. multifiliis ) and relatively large gene complements (20–30 protein-coding genes) [ 39 , 41 , 44 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture

Zhang

et al. 2021

IJMS

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Determination and comparisons of complete mitochondrial genomes (mitogenomes) are important to understand the origin and evolution of mitochondria. Mitogenomes of unicellular protists are particularly informative in this regard because they are gene-rich and display high structural diversity. Ciliates are a highly diverse assemblage of protists and their mitogenomes (linear structure with high A+T content in general) were amongst the first from protists to be characterized and have provided important insights into mitogenome evolution. Here, we report novel mitogenome sequences from three representatives (Strombidium sp., Strombidium cf. sulcatum, and Halteria grandinella) in two dominant ciliate lineages. Comparative and phylogenetic analyses of newly sequenced and previously published ciliate mitogenomes were performed and revealed a number of important insights. We found that the mitogenomes of these three species are linear molecules capped with telomeric repeats that differ greatly among known species. The genomes studied here are highly syntenic, but larger in size and more gene-rich than those of other groups. They also all share an AT-rich tandem repeat region which may serve as the replication origin and modulate initiation of bidirectional transcription. More generally we identified a split version of ccmf, a cytochrome c maturation-related gene that might be a derived character uniting taxa in the subclasses Hypotrichia and Euplotia. Finally, our mitogenome comparisons and phylogenetic analyses support to reclassify Halteria grandinella from the subclass Oligotrichia to the subclass Hypotrichia. These results add to the growing literature on the unique features of ciliate mitogenomes, shedding light on the diversity and evolution of their linear molecular architecture.

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Section: Introductionmentioning

confidence: 99%

Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture

Zhang

et al. 2021

IJMS

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“…Compared with mitochondrial studies on human diseases and the breeding of animals and plants ( 28 – 32 ), attention to mitochondria shows a much slower growth in ciliates. Since the first reports on mitochondrial DNA of Tetrahymena thermophila , Paramecium primaurelia, and Paramecium tetraurelia in the 1980s ( 33 , 34 ), mitogenomes of approximately 30 species from the Oligohymenophorea ( 35 ), Spirotrichea ( 36 ), Heterotrichea ( 37 ), and Armophorea ( 38 ) classes have been documented. However, this constitutes only a small fraction when considering the tens of thousands of ciliate species, and population-level investigation remains nearly unstudied ( 39 ).…”

Section: Introductionmentioning

confidence: 99%

Mitogenomic architecture and evolution of the soil ciliates Colpoda

Zhang,

Li,

Wang

et al. 2024

mSystems

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Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28 – 33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes. IMPORTANCE Colpoda , one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.

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Novel findings on the mitochondria in ciliates, with description of mitochondrial genomes of six representatives

Zhang,

Fu,

et al. 2024

Mar Life Sci Technol

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Determining and comparing mitochondrial genomes (mitogenomes) are essential for assessing the diversity and evolution of mitochondria. Ciliates are ancient and diverse unicellular eukaryotes, and thus are ideal models for elucidating the early evolution of mitochondria. Here, we report on six new mitogenomes of spirotrichs, a dominant ciliate group, and perform comparative analyses on 12 representative species. We show that: (1) the mitogenomes of spirotrichs are linear structures with high A+T contents (61.12–81.16%), bidirectional transcription, and extensive synteny (except for the nad5, ccmf and cob genes in Euplotia); (2) the non-split of NADH dehydrogenase subunit 2 gene (nad2) is a plesiomorphy of ciliates, whereas it has evolved into a split gene in Spirotrichea (apart from Euplotes taxa), Oligohymenophorea, and Armophorea; (3) the number of small subunit ribosomal proteins (rps) encoded in mitogenomes increases in the later branching classes of ciliates, whereas rps8 shows a loss trend during the evolution of Euplotes taxa; (4) the mitogenomes of spirotrichs exhibit A/T codon bias at the third position, and the codon bias is mainly due to DNA mutation in oligotrichs, hypotrichs and Diophrys appendiculata; (5) the phylogenetic position of D. appendiculata is unstable and controversial based on both phylogenetic analyses and mitogenome evidence. In summary, we investigated the mitogenome diversity of spirotrichs and broadened our understanding of the evolution of mitochondria in ciliates.

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The complete mitochondrial genome of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 (Ciliophora: Heterotrichea)

Cited by 4 publications

References 17 publications

Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture

Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture

Mitogenomic architecture and evolution of the soil ciliates Colpoda

Novel findings on the mitochondria in ciliates, with description of mitochondrial genomes of six representatives

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