Evolutionary Rates of Bumblebee Genomes Are Faster at Lower Elevations.
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ABSTRACT:
SUBMITTER: Lin G
PROVIDER: S-EPMC6526908 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
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Project description:Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial DNAs. However, much of the plastid-containing eukaryotic diversity falls outside of land plants, and the patterns of plastid DNA evolution for embryophytes do not necessarily reflect those of other groups. Recent analyses of plastid and mitochondrial substitution rates in diverse lineages have uncovered very different trends than those recorded for land plants. Here, I explore these new data and argue that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae. These findings have far-reaching implications for how we view plastid genomes and how their sequences are used for evolutionary analyses, and might ultimately reflect a general tendency toward more efficient DNA repair mechanisms in plastids than in mitochondria.
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Project description:This experiment provide a comprehensive overview of proteins present in bumblebee venom.
2015-04-29 | PXD001623 | Pride
Project description:Resistance to the frontline antibiotic rifampicin constitutes a challenge to the treatment and control of tuberculosis. Here, we analyzed the mutational landscape of Mycobacterium smegmatis during long-term evolution with increasing concentrations of rifampicin, using a mutation accumulation assay combined with whole-genome sequencing. Antibiotic treatment enhanced the acquisition of mutations, doubling the genome-wide mutation rate of the wild-type cells. While antibiotic exposure led to extinction of almost all wild-type lines, the hypermutable phenotype of the ΔnucS mutant strain (noncanonical mismatch repair deficient) provided an efficient response to the antibiotic, leading to high rates of survival. This adaptative advantage resulted in the emergence of higher levels of rifampicin resistance, an accelerated acquisition of drug resistance mutations in rpoB (β RNA polymerase), and a wider diversity of evolutionary pathways that led to drug resistance. Finally, this approach revealed a subset of adaptive genes under positive selection with rifampicin that could be associated with the development of antibiotic resistance. IMPORTANCE Rifampicin is the most important first-line antibiotic against mycobacterial infections, including tuberculosis, one of the top causes of death worldwide. Acquisition of rifampicin resistance constitutes a major global public health problem that makes the control of the disease challenging. Here, we performed an experimental evolution assay under antibiotic selection to analyze the response and adaptation of mycobacteria, leading to the acquisition of rifampicin resistance. This approach explored the total number of mutations that arose in the mycobacterial genomes under long-term rifampicin exposure, using whole-genome sequencing. Our results revealed the effect of rifampicin at a genomic level, identifying different mechanisms and multiple pathways leading to rifampicin resistance in mycobacteria. Moreover, this study detected that an increase in the rate of mutations led to enhanced levels of drug resistance and survival. In summary, all of these results could be useful to understand and prevent the emergence of drug-resistant isolates in mycobacterial infections.
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Project description:BackgroundThe rise of the primate lineage is accompanied by an outstanding emergence of microRNAs, small non-coding RNAs with a prominent role in gene regulation. In spite of their biological importance little is known about the way in which natural selection has influenced microRNAs in the human lineage. To study the recent evolutionary history of human microRNAs and to analyze the signatures of natural selection in genomic regions harbouring microRNAs we have investigated the nucleotide substitution rates of 1,872 human microRNAs in the human and chimpanzee lineages.ResultsWe produced a depurated set of microRNA alignments of human, chimpanzee and orang-utan orthologs combining BLAT and liftOver and selected 1,214 microRNA precursors presenting optimal secondary structures. We classified microRNAs in categories depending on their genomic organization, duplication status and conservation along evolution. We compared substitution rates of the aligned microRNAs between human and chimpanzee using Tajima's Relative Rate Test taking orang-utan as out-group and found several microRNAs with particularly high substitution rates in either the human or chimpanzee branches. We fitted different models of natural selection on these orthologous microRNA alignments and compared them using a likelihood ratio test that uses ancestral repeats and microRNA flanking regions as neutral sequences. We found that although a large fraction of human microRNAs is highly conserved among the three species studied, significant differences in rates of molecular evolution exist among microRNA categories. Particularly, primate-specific microRNAs, which are enriched in isolated and single copy microRNAs, more than doubled substitution rates of those belonging to older, non primate-specific microRNA families.ConclusionsOur results corroborate the remarkable conservation of microRNAs, a proxy of their functional relevance, and indicate that a subset of human microRNAs undergo nucleotide substitutions at higher rates, which may be suggestive of the action of positive selection.
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Project description:Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
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Project description:BackgroundThe shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.ResultsWe report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.ConclusionsThese two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
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Project description:In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation.
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