The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

D’Elia, Domenica; Catalano, Domenico; Licciulli, Flavio; Turi, Antonio; Tripoli, Gaetano; Porcelli, Damiano; Saccone, Cecilia; Caggese, Corrado

doi:10.1016/j.mito.2006.07.001

Cited by 21 publications

(16 citation statements)

References 17 publications

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“…()]; 133 genes involved in cytonuclear interactions [identified from mitodrome , D'Elia et al . (), and mitores , Catalano et al . (), in Drosophila ]; 30 reproduction‐related genes, 20 habitat‐related genes (because of the known association with wave action, proteins from the foot, the byssus filament and adhesive plaques are suspected to be involved with habitat specialization) and six nucleoporines (following Nolte et al .…”

Section: Methodsmentioning

confidence: 99%

Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

et al. 2015

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Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genomewide patterns of introgression in Mytilus and that gene flow between different species, with contiguous ranges, explained up to half of the intraspecific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, for example Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganization of genetic backgrounds, needs to be more widely considered to make better sense of genome scans.

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Section: Methodsmentioning

confidence: 99%

Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

et al. 2015

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“…In addition to the analyses of the global gene set, genes encoding OXPHOS-related proteins (complexes I, II, III, IV, and ATP synthase) were selected for closer examination because these are putative targets of mitochondrial variation. Both mtDNA and nuclear genes targeted to the mitochondrion were downloaded from the MitoDrome database ( Sardiello et al 2003 ; D’Elia et al 2006 ). Arc diagrams were used to display the relationship between various genes in the OXPHOS pathway in D. melanogaster ( Tripoli et al 2005 ) and the effect of alternative mtDNA haplotype in each nuclear background and in each sex.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles inDrosophila

Mossman

Tross

et al. 2016

Genetics

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The assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. Here we tested how the transcriptome responds to mtDNA and nDNA variation, along with mitonuclear interactions (mtDNA × nDNA) in Drosophila melanogaster. We used two mtDNA haplotypes that differ in a substantial number of single nucleotide polymorphisms, with >100 amino acid differences. We placed each haplotype on each of two D. melanogaster nuclear backgrounds and tested for transcription differences in both sexes. We found that large numbers of transcripts were differentially expressed between nuclear backgrounds, and that mtDNA type altered the expression of nDNA genes, suggesting a retrograde, trans effect of mitochondrial genotype. Females were generally more sensitive to genetic perturbation than males, and males demonstrated an asymmetrical effect of mtDNA in each nuclear background; mtDNA effects were nuclear-background specific. mtDNA-sensitive genes were not enriched in male- or female-limited expression space in either sex. Using a variety of differential expression analyses, we show the responses to mitonuclear covariation to be substantially different between the sexes, yet the mtDNA genes were consistently differentially expressed across nuclear backgrounds and sexes. Our results provide evidence that the main mtDNA effects can be consistent across nuclear backgrounds, but the interactions between mtDNA and nDNA can lead to sex-specific global transcript responses.

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“…We identified 59 of the 65 OXPHOS pathway subunit genes known from Drosophila (MitoDrome database; D'Elia et al ., 2006) in the Nasonia genome (Table 1; Supp. I).…”

Section: Resultsmentioning

confidence: 99%

“…For each nuclear encoded gene of the five OXPHOS complexes, we obtained the Drosophila melanogaster protein sequence from the MitoDrome database (D'Elia et al ., 2006; http://www2.ba.itb.cnr.it/MitoDrome/). These sequences were used as queries to search the Nasonia genome assembly 1.0 (Werren et al ., in press) using the program TBLASTN and applying the SEG filter for low complexity sequences (Altschul et al , 1997).…”

Section: Methodsmentioning

confidence: 99%

Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia

et al. 2010

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The principal energy generating system in animals is the oxidative phosphorylation (OXPHOS) pathway, which depends on the tight interaction of nuclear and mitochondrial encoded genes to function properly. Mitochondrial genes accumulate substitutions more quickly than nuclear genes, yet the impact of selection on mitochondrial genes is significantly reduced relative to nuclear genes due to the non-recombining nature of the mitochondrial genome and its predicted smaller effective population size. It has therefore been hypothesized that the nuclear encoded genes of the OXPHOS pathway are under strong selective pressure to compensate for the accumulation of deleterious nucleotide substitutions in mitochondrial encoded OXPHOS genes; a process known as compensatory co-adaptation. We evaluated this hypothesis by analyzing nuclear encoded OXPHOS genes for signatures of positive selection as well as evolutionary constraints at amino acid sites. We considered OXPHOS genes of six holometabolous insects and their orthologs from three Nasonia parasitoid wasps; hybrids of which suffer from an increased mortality rate caused by cytonuclear genic incompatibilities. Although nuclear OXPHOS genes are typically highly conserved, we found significant evidence for elevated amino acid divergence in four of the 59 studied nuclear encoded OXPHOS genes. We also found that three of these four genes, as well as six other OXPHOS genes, contain amino acid substitutions between Nasonia species at evolutionarily constrained sites. It is possible that these genes account for the reported incompatibility in Nasonia hybrids and their characterization may lead to a better understanding of the role of positive selection in the genetics of speciation.

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The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

Cited by 21 publications

References 17 publications

Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles inDrosophila

Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia

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