Mitochondrial Recombination Reveals Mito–Mito Epistasis in Yeast

AbstractPlant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pre-genome, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about a third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly-studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

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mtDNA recombination indicative of hybridization suggests a role of the mitogenome in the adaptation of reef-building corals to extreme environments

10.1101/462069 ◽

2018 ◽

Cited By ~ 1

Author(s):

Eulalia Banguera-Hinestroza ◽

Yvonne Sawall ◽

Abdulmohsin Al-Sofyani ◽

Patrick Mardulyn ◽

Javier Fuertes-Aguilar ◽

...

Keyword(s):

Indian Ocean ◽

Red Sea ◽

Arabian Gulf ◽

Extreme Environments ◽

Introgressive Hybridization ◽

Gulf Of Aden ◽

Mitochondrial Recombination ◽

Geographic Ranges ◽

Mtdna Recombination ◽

Ancestral Lineage

AbstractmtDNA recombination following hybridization is rarely found in animals and was never until now reported in reef-building corals. Here we report unexpected topological incongruence among mitochondrial markers as evidence of mitochondrial introgression in the phylogenetic history of Stylophora species distributed along broad geographic ranges. Our analyses include specimens from the Indo-Pacific, the Indian Ocean and the full latitudinal (2000 km) and environmental gradient (21°C-33°C) of the Red Sea (N=827). The analysis of Stylophora lineages in the framework of the mitogenome phylogenies of the family Pocilloporidae, coupled with analyses of recombination, shows the first evidence of asymmetric patterns of introgressive hybridization associated to mitochondrial recombination in this genus. Hybridization likely occurred between an ancestral lineage restricted to the Red Sea/Gulf of Aden basins and migrants from the Indo-Pacific/Indian Ocean that reached the Gulf of Aden. The resulting hybrid lives in sympatry with the descendants of the parental Red Sea lineage, from which it inherited most of its mtDNA (except a highly variable recombinant region that includes the nd6, atp6, and mtORF genes) and expanded its range into the hottest region of the Arabian Gulf, where it is scarcely found. Noticeably, across the Red Sea both lineages exhibit striking differences in terms of phylogeographic patterns, clades-morphospecies association, and zooxanthellae composition. Our data suggest that the early colonization of the Red Sea by the ancestral lineage, which involved overcoming multiple habitat changes and extreme temperatures, resulted in changes in mitochondrial proteins, which led to its successful adaptation to the novel environmental conditions.

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Mitochondrial Recombination?

Science ◽

10.1126/science.284.5423.2089e ◽

1999 ◽

Vol 284 (5423) ◽

pp. 2089e-2089 ◽

Cited By ~ 12

Author(s):

P. Arctander

Keyword(s):

Mitochondrial Recombination

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Mitochondrial recombination in cytoplasmic hybrids of Nicotiana tabacum by protoplast fusion

Nature ◽

10.1038/281401a0 ◽

1979 ◽

Vol 281 (5730) ◽

pp. 401-403 ◽

Cited By ~ 307

Author(s):

Geneviève Belliard ◽

Fernand Vedel ◽

Georges Pelletier

Keyword(s):

Nicotiana Tabacum ◽

Protoplast Fusion ◽

Mitochondrial Recombination ◽

Cytoplasmic Hybrids

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Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

mBio ◽

10.1128/mbio.00868-15 ◽

2015 ◽

Vol 6 (5) ◽

Cited By ~ 62

Author(s):

Rhys A. Farrer ◽

Christopher A. Desjardins ◽

Sharadha Sakthikumar ◽

Sharvari Gujja ◽

Sakina Saif ◽

...

Keyword(s):

Positive Selection ◽

Species Complex ◽

Cryptococcus Gattii ◽

Genomic Variation ◽

Pulmonary Infections ◽

Copper Transporter ◽

Mitochondrial Recombination ◽

Content Type ◽

Multidrug Transporters ◽

Gene Expansion

ABSTRACT Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, and compared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. Through inclusion of population-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrial recombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur protein aconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positive selection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex. IMPORTANCE The genetic differences between phenotypically different pathogens provide clues to the underlying mechanisms of those traits and can lead to new drug targets and improved treatments for those diseases. In this paper, we compare 16 genomes belonging to four highly differentiated lineages of Cryptococcus gattii, which cause pulmonary infections in otherwise healthy humans and other animals. Half of these lineages have not had their genomes previously assembled and annotated. We identified 15 ancestral rearrangements in the genome and over 700 genes that are unique to one or more lineages, many of which are associated with virulence. In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters. Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex.

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Mitochondrial Recombination

Encyclopedia of Genetics, Genomics, Proteomics and Informatics ◽

10.1007/978-1-4020-6754-9_10541 ◽

2008 ◽

pp. 1235-1236

Keyword(s):

Mitochondrial Recombination

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Mitochondrial recombination in crosses of iso- and anisomitochondrial saccharomyces cerevisiae

Molecular and Cellular Biochemistry ◽

10.1007/bf01734161 ◽

1977 ◽

Vol 14 (1-3) ◽

pp. 25-29

Author(s):

Jaak Kaldma

Keyword(s):

Saccharomyces Cerevisiae ◽

Mitochondrial Recombination

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ABSENCE OF DETECTABLE MITOCHONDRIAL RECOMBINATION IN PARAMECIUM

Genetics ◽

10.1093/genetics/93.4.797 ◽

1979 ◽

Vol 93 (4) ◽

pp. 797-831

Author(s):

André Adoutte ◽

Jonathan K Knowles ◽

Annie Sainsard-Chanet

Keyword(s):

Antibiotic Resistance ◽

Large Scale ◽

Nuclear Gene ◽

Paramecium Tetraurelia ◽

Wild Type ◽

Resistance Mutations ◽

Mitochondrial Recombination ◽

Mitochondrial Ribosomes ◽

Molecular Alterations ◽

Resistance Markers

ABSTRACT An extensive search for recombination between mitochondrial markers was carried out in Paramecium tetraurelia. Thirty-two combinations, altogether involving 24 different markers, were studied. The markers belonged to the three main categories of mitochondrial mutations presently available in this organism. (a) Spontaneous or UV-induced antibiotic resistance mutations, most probably affecting mitochondrial ribosomes, (b) nitrowguanidine-induced antibiotic resistance markers displaying thermosensitivity or slow growth, enabling easy selection of possible wild-type recombinants, and (c) mitochondrial partial suppressors of a nuclear gene, probably corresponding to molecular alterations distinct from the preceding two categories. In addition, different genetic configurations were analyzed (i e., mutant x mutant, double-mutant x wild-type, etc.).——None of the combinations yielded any evidence for the occurrence of recombined genomes despite the fact that: (1) all of them were studied on a large scale involving the screening of at least several thousand mitochondrial genomes (often several millions), (2) in many of them the detection level was sufficiently high to enable the isolation of spontaneous mutants in control cells, and (3) in several of them, reconstitution experiments carried out in parallel show that the conditions were fully adequate to detect recombinant genotypes. The results are in marked contrast with those obtained on the few other organisms in which mitochondrial recombination has been studied, particularly Saccharomyces cerevisiae, in which mitochondrial recombination is intense.——The most likely basis for the various manifestations of mitochondrial genetic autonomy in Paramecium, described in this as well as in previous publications, is that the chondriome of this organism is made up of thousands of structurally discrete, noninteracting units.

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