The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs

<p>Abstract</p> <p>Background</p> <p>The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of <it>Panonychus citri </it>(Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari.</p> <p>Results</p> <p>The mitochondrial genome of <it>P. citri </it>is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs), a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for <it>P. citri </it>is the same as those for <it>P. ulmi </it>and <it>Tetranychus urticae</it>, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the <it>P. citri </it>mitochondrial genome has a high A + T content (85.28%), which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03). The Acari mitochondrial <it>nad1 </it>exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of <it>P. citri </it>are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp), lacking either the T- or D-arm, as found in <it>P. ulmi</it>, <it>T. urticae</it>, and other Acariform mites.</p> <p>Conclusions</p> <p>The <it>P. citri </it>mitochondrial gene order is markedly different from those of other chelicerates, but is conserved within the family Tetranychidae indicating that high rearrangements have occurred after Tetranychidae diverged from other Acari. Comparative analyses suggest that the genome size, gene order, gene content, codon usage, and base composition are strongly variable among Acari mitochondrial genomes. While extremely small and unusual tRNA genes seem to be common for Acariform mites, further experimental evidence is needed.</p

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.Comment: 41 pages, 5 figure

The pace-of-life : A sex-specific link between metabolic rate and life history in bean beetles

Metabolic rate (MR) is a key functional trait simply because metabolism converts resources into population growth rate. Yet, our empirical understanding of the sources of within species variation in MR, as well as of its life history and ecological correlates, is rather limited. Here, we assess whether MR lies at the root of a syndrome of correlated rate-dependent life-history traits in an insect. Selection for early (E) or late (L) age-at-reproduction for &gt;160 generations in the bean beetle Acanthoscelides obtectus has produced beetles that differ markedly in juvenile development, body size, fecundity schedules, ageing and life span. Here, we use micro-respirometry to test whether this has been associated with the evolution of age- and sex-specific metabolic phenotypes. We find that mass-specific MR is 18% higher in E lines compared to L lines and that MR decreases more rapidly with chronological, but not biological, age in E lines. Males, under sexual selection to “live-fast-die-young”, show 50% higher MR than females and MR decreased more rapidly with age in males. Our results are consistent with a central role for MR for the divergence in “pace-of-life” seen in these beetles, supporting the view that MR lies at the root of ecologically relevant life-history trait variation within species

Lactate dehydrogenase and glycerol-3-phosphate dehydrogenase cooperatively regulate growth and carbohydrate metabolism during Drosophila melanogaster larval development

The dramatic growth that occurs during Drosophila larval development requires rapid conversion of nutrients into biomass. Many larval tissues respond to these biosynthetic demands by increasing carbohydrate metabolism and lactate dehydrogenase (LDH) activity. The resulting metabolic program is ideally suited for synthesis of macromolecules and mimics the manner by which cancer cells rely on aerobic glycolysis. To explore the potential role of Drosophila LDH in promoting biosynthesis, we examined how Ldh mutations influence larval development. Our studies unexpectedly found that Ldh mutants grow at a normal rate, indicating that LDH is dispensable for larval biomass production. However, subsequent metabolomic analyses suggested that Ldh mutants compensate for the inability to produce lactate by generating excess glycerol-3-phosphate (G3P), the production of which also influences larval redox balance. Consistent with this possibility, larvae lacking both LDH and G3P dehydrogenase (GPDH1) exhibit growth defects, synthetic lethality and decreased glycolytic flux. Considering that human cells also generate G3P upon inhibition of lactate dehydrogenase A (LDHA), our findings hint at a conserved mechanism in which the coordinate regulation of lactate and G3P synthesis imparts metabolic robustness to growing animal tissues

Beyond the Powerhouse: Integrating Mitonuclear Evolution, Physiology, and Theory in Comparative Biology

Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this symposium volume, scientists working in diverse organismal systems spanning vast biological scales address emerging topics in integrative, comparative biology in light of mitonuclear interactions

Reduction in the cumulative effect of stress-induced inbreeding depression due to intragenerational purging in Drosophila melanogaster

Environmental stress generally exacerbates the harmful effects of inbreeding and it has been proposed that this could be exploited in purging deleterious alleles from threatened inbred populations. However, understanding what factors contribute to variability in the strength of inbreeding depression (ID) observed across adverse environmental conditions remains a challenge. Here, we examined how the nature and timing of stress affects ID and the potential for purging using inbred and outbred Drosophila melanogaster larvae exposed to biotic (larval competition, bacteria infection) and abiotic (ethanol, heat) stressors compared with unstressed controls. ID was measured during (larval survival) and after (male mating success) stress exposure. The level of stress imposed by each stressor was approximately equal, averaging a 42% reduction in outbred larval survival relative to controls. All stressors induced on average the same ID, causing a threefold increase in lethal equivalents for larval survival relative to controls. However, stress-induced ID in larval success was followed by a 30% reduction in ID in mating success of surviving males. We propose that this fitness recovery is due to ‘intragenerational purging' whereby fitness correlations facilitate stress-induced purging that increases the average fitness of survivors in later life history stages. For biotic stressors, post-stress reductions in ID are consistent with intragenerational purging, whereas for abiotic stressors, there appeared to be an interaction between purging and stress-induced physiological damage. For all stressors, there was no net effect of stress on lifetime ID compared with unstressed controls, undermining the prediction that stress enhances the effectiveness of population-level purging across generations