Mitochondrial genome structure of photosynthetic eukaryotes

Yurina, N. P.; Odintsova, M. S.

doi:10.1134/s0006297916020048

Cited by 15 publications

(10 citation statements)

References 44 publications

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“…Furthermore, mitochondrial genome expansion is less frequent in green algae compared with plants (Mower, Sloan & Alverson, 2012). While Zheng et al (2018) did not propose an evolutionary explanation for these findings, the inflated noncoding regions described are consistent with previous studies in plants showing that the variation in the sizes of their mitochondrial genomes is predominantly explained by changes in noncoding DNA content including repeats, introns, intergenic DNA and DNA of foreign origin (Yurina & Odintsova, 2016). Therefore, the mitochondrial genome of C. lentillifera provides an interesting case in the Chlorophyta to examine the evolution of organellar genomes and, in particular, the processes driving genome expansion.…”

Section: Introductionsupporting

confidence: 86%

“…Although they share many unifying features, the green algae (Chlorophyta) are a diverse group with genomes that vary considerably in structure and gene content (Yurina & Odintsova, 2016). Most work on Chlorophyta genomes to date has focused on organellar genomes, with in excess of 150 chloroplast and 70 mitochondrial genomes published on GenBank.…”

Section: Introductionmentioning

confidence: 99%

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The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

Repetti

Jackson

Judd

et al. 2020

PeerJ

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Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.

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Section: Introductionsupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

Repetti

Jackson

Judd

et al. 2020

PeerJ

View full text Add to dashboard Cite

show abstract

“…In the baker’s yeast, S. cerevisiae, it exists predominantly as polydisperse linear tandem arrays, and circular forms represent a minority, while in Candida albicans , mtDNA forms a branched network [20,21,22,23]. The much larger mitochondrial genomes of plants show even higher variability of organization, including plasmids replicating independently of the main mitochondrial genome [24]. While the mitochondrial genomes in most metazoans are circular, protists, cnidaria, and sponges have typically differently organized mitochondrial genomes, including concatenated circles, linear concatemers, or multipartite genomes, sometimes co-existing within the same species [19,25,26,27,28].…”

Section: Topoisomerase Requirements In Mitochondrial Dna Maintenancementioning

confidence: 99%

Twist and Turn—Topoisomerase Functions in Mitochondrial DNA Maintenance

Goffart

Hangas

Pohjoismäki

2019

IJMS

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Like any genome, mitochondrial DNA (mtDNA) also requires the action of topoisomerases to resolve topological problems in its maintenance, but for a long time, little was known about mitochondrial topoisomerases. The last years have brought a closer insight into the function of these fascinating enzymes in mtDNA topology regulation, replication, transcription, and segregation. Here, we summarize the current knowledge about mitochondrial topoisomerases, paying special attention to mammalian mitochondrial genome maintenance. We also discuss the open gaps in the existing knowledge of mtDNA topology control and the potential involvement of mitochondrial topoisomerases in human pathologies. While Top1mt, the only exclusively mitochondrial topoisomerase in mammals, has been studied intensively for nearly a decade, only recent studies have shed some light onto the mitochondrial function of Top2β and Top3α, enzymes that are shared between nucleus and mitochondria. Top3α mediates the segregation of freshly replicated mtDNA molecules, and its dysfunction leads to mtDNA aggregation and copy number depletion in patients. Top2β, in contrast, regulates mitochondrial DNA replication and transcription through the alteration of mtDNA topology, a fact that should be acknowledged due to the frequent use of Topoisomerase 2 inhibitors in medical therapy.

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“…Recent phylogenomic studies of Cuscuta generally focused on their plastid genome and revealed extensive levels of gene loss, especially regarding the ndh gene family ( Braukmann et al 2013 ; Banerjee and Stefanović 2019 , 2020 ). Compared with plastid genomes, mitochondrial genomes of plants evolve more slowly at the DNA substitution level, and generally do not experience substantial gene losses ( Knoop 2004 ; Yurina and Odintsova 2016 ; Lin 2020 ). However, plant mitochondrial genomes undergo frequent fusion and recombination, and often incorporate sequences from their own plastid or nuclear genomes, obtained through intracellular gene transfer (e.g., Stern and Lonsdale 1982 ; Schuster and Brennicke 1987 ).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Phylogenomics of Cuscuta (Convolvulaceae) Reveals a Potentially Functional Horizontal Gene Transfer from the Host

Lin

Banerjee

Stefanović

2022

Genome Biology and Evolution

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Horizontal gene transfers (HGTs) from host or other organisms have been reported in mitochondrial genomes of parasitic plants. Genes transferred in this fashion have usually been found non-functional. Several examples of HGT from the mitochondrial genome of parasitic Cuscuta (Convolvulaceae) to its hosts have been reported, but not vice versa. Here we used 31 protein-coding mitochondrial genes to infer the phylogeny of Cuscuta, and compared it with previous nuclear and plastid phylogenetic estimates. We also investigated the presence of HGTs within these lineages. Unlike in plastid genomes, we did not find extensive gene loss in their mitochondrial counterparts. Our results reveal the first example of organellar HGT from host to Cuscuta. Mitochondrial atp1 genes of South African subgenus Pachystigma were inferred to be transferred from Lamiales, with high support. Moreover, the horizontally transferred atp1 gene has functionally replaced the native, vertically transmitted copy, has an intact open reading frame, and is under strong purifying selection, all of which suggests that this xenolog remains functional. The mitochondrial phylogeny of Cuscuta is generally consistent with previous plastid and nuclear phylogenies, except for the misplacement of Pachystigma when atp1 is included. This incongruence may be caused by the HGT mentioned above. No example of HGT was found within mitochondrial genes of three other, independently evolved parasitic lineages we sampled: Cassytha/Laurales, Krameria/Zygophyllales, and Lennooideae/Boraginales.

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Mitochondrial genome structure of photosynthetic eukaryotes

Cited by 15 publications

References 44 publications

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

Twist and Turn—Topoisomerase Functions in Mitochondrial DNA Maintenance

Mitochondrial Phylogenomics of Cuscuta (Convolvulaceae) Reveals a Potentially Functional Horizontal Gene Transfer from the Host

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