Fierst.Dryad

Simulation result

Data from: A history of phenotypic plasticity accelerates adaptation to a new environment

Can a history of phenotypic plasticity increase the rate of adaptation to a new environment? Theory suggests it can through two different mechanisms. Phenotypically plastic organisms can adapt rapidly to new environments through genetic assimilation, or the fluctuating environments that result in phenotypic plasticity can produce evolvable genetic architectures. In this article, I studied a model of a gene regulatory network that determined a phenotypic character in one population selected for phenotypic plasticity and a second population in a constant environment. A history of phenotypic plasticity increased the rate of adaptation in a new environment, but the amount of this increase was dependent on the strength of selection in the original environment. Phenotypic variance in the original environment predicted the adaptive capacity of the trait within, but not between, plastic and non-plastic populations. These results have implications for invasive species, and ecological studies of rapid adaptation

Fierst.Dryad

Simulation result

Decontaminating eukaryotic genome assemblies with machine learning

Abstract Background High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few existing methods for rigorously decontaminating eukaryotic assemblies. Those that do exist filter sequences based on nucleotide similarity to contaminants and risk eliminating sequences from the target organism. Results We introduce a novel application of an established machine learning method, a decision tree, that can rigorously classify sequences. The major strength of the decision tree is that it can take any measured feature as input and does not require a priori identification of significant descriptors. We use the decision tree to classify de novo assembled sequences and compare the method to published protocols. Conclusions A decision tree performs better than existing methods when classifying sequences in eukaryotic de novo assemblies. It is efficient, readily implemented, and accurately identifies target and contaminant sequences. Importantly, a decision tree can be used to classify sequences according to measured descriptors and has potentially many uses in distilling biological datasets

Rebalancing Redox to Improve Biobutanol Production by Clostridium tyrobutyricum

Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in Clostridium tyrobutyricum via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production. The objective of this study was to improve butanol production by rebalancing redox. Firstly, a metabolically-engineered mutant CTC-fdh-adhE2 was constructed by introducing heterologous formate dehydrogenase (fdh) and bifunctional aldehyde/alcohol dehydrogenase (adhE2) simultaneously into wild-type C. tyrobutyricum. The mutant evaluation indicated that the fdh-catalyzed NADH-producing pathway improved butanol titer by 2.15-fold in the serum bottle and 2.72-fold in the bioreactor. Secondly, the medium supplements that could shift metabolic flux to improve the production of butyrate or butanol were identified, including vanadate, acetamide, sodium formate, vitamin B12 and methyl viologen hydrate. Finally, the free-cell fermentation produced 12.34 g/L of butanol from glucose using the mutant CTC-fdh-adhE2, which was 3.88-fold higher than that produced by the control mutant CTC-adhE2. This study demonstrated that the redox engineering in C. tyrobutyricum could greatly increase butanol production

De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species

Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se

Whole chromosome comparisons among <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>.

<p>The <i>C. remanei</i> The linkage map was sufficient to assemble and order 98.93% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome X, 78.38% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome II and 81.40% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome IV. (a) <i>C. remanei</i> linkage groups were assigned to chromosomes based on gene orthology to <i>C. elegans</i> chromosomes. Reproductive incompatibility between the <i>C. remanei</i> strains used to construct the linkage map resulted in over-dispersion of the linkage map and 13 linkage groups instead of the 6 chromosomes expected (both <i>C. elegans</i> and <i>C. briggsae</i> have 6 chromosomes, respectively). (b) The cumulative size and orthologous gene alignments for scaffolds that were not assigned to linkage groups. c-e) Orthologous gene alignments indicated blocks of syntenic DNA between <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>. The panels c-e show orthologous genes on chromosomes X, II, and IV, with chromosome size scaled to linkage group size in <i>C. remanei</i> (X 18.5Mb, II 12.5Mb, IV 14.5 Mb). Orthologous genes were connected between species pairs, and grouped together if the genes were within 50,000 nucleotides of each other. Single gene translocations were excluded for clarity. Green indicates orthologs identified between <i>C. elegans</i> and <i>C. remanei</i>, blue indicates orthologs identified between <i>C. remanei</i> and <i>C. briggsae</i>, and grey indicates orthologs identified between <i>C. briggsae</i> and <i>C. elegans</i>. The outer rings are chromosomes X, II, and IV in each species. Each gray line is an orthologous gene located on the same chromosome in the other species and each black line is an orthologous gene that is located on a different chromosome in one of the other species. There are few blocks of interchromosomal translocation, and few black lines. White indicates regions of the chromosome where there were no orthologous genes identified between the species. (c) There was a large region of divergence (roughly 3.6Mb) on the <i>C. remanei</i> X; (d) Chromosome II is not completely assembled in <i>C. remanei</i>, and there were several regions of <i>C. elegans</i> and <i>C. briggsae</i> chromosome II that were not represented in <i>C. remanei</i>; (e) Chromosome IV.</p