Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we ...explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.
One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S–5.8S–26S nuclear ribosomal ...cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based
exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.
Polyploidy, the condition of possessing more than 2 complete chromosome sets in the same nucleus, is frequent in nature and has implications for a species' prospects for evolution. Newly formed ...polyploids, so-called neopolyploids, undergo a wide spectrum of genomic changes upon genome merger and duplication. Here, we review recent literature describing genomic and transcriptomic changes along the pathway from neoallopolyploid formation to the stabilization of species and diversification at the allopolyploid level. We begin by reviewing pathways of polyploid formation and discuss the effects of genome doubling and hybridization on chromosome pairing. We then review our knowledge of epigenetic changes in allopolyploids, followed by a consideration of the effects of these structural genomic and epigenetic changes on the transcriptional activity of genes in allopolyploids. We discuss the effects of changes in gene expression in polyploids with respect to current evolutionary theory. Finally, we draw attention to the general question of the relationships between genomic and transcriptomic alteration and incipient diversification among sibling polyploid lines and populations.
Although scholars often assume that Luke and Justin similarly claim the sacred texts of Jews for the non-Jewish church, this book offers a fresh analysis that uncovers significant differences between ...their respective depictions of the relationship between Christ-believers and the Jewish scriptures.
Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we ...explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.
Affective states alter the perception of how quickly time is passing. However, previous studies have not examined the independent and interactive effects of emotion and time perception on behavioral ...outcomes. The current study sought to better understand the relationships between affect, time perception, and reported engagement in COVID-19 pathogen avoidance behaviors (e.g., social distancing, wearing a mask) over 1 year. The study sample was comprised of American adults (n = 1,000) recruited using Prolific. The majority of participants in the final sample (50.1% male, 46.8% female, 3.1% nonbinary/other) identified as White/Caucasian (78.9%) or Black/African American (11.9%). The average age in the sample was 34.4 years (SD = 11.3). Consistent with study hypotheses, approach-motivated affective states (happiness) were associated with time flying, and avoidance-motivated affective states (nervous, lack of control) were associated with time dragging. Moderation analyses revealed that reports of greater avoidance-motivated affect and time dragging, and reports of greater approach-motivated affect and time flying interacted to predict more frequent engagement in pathogen avoidance behaviors. These results contribute to the existing literature describing the affective and behavioral effects of the COVID-19 pandemic by suggesting both approach- and avoidance-motivated affective states have important implications for engagement in pathogen avoidance behaviors.
Genome doubling, or polyploidy, is a major factor accounting for duplicate genes found in most eukaryotic genomes. Polyploidy has considerable effects on duplicate gene expression, including ...silencing and up- or downregulation of one of the duplicated genes. These changes can arise with the onset of polyploidization or within several generations after polyploid formation and they can have epigenetic causal factors. Many expression alterations are organ-specific. Specific genes can be independently and repeatedly silenced during polyploidization, whereas patterns for other genes appear to be more stochastic. Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of gene expression changes that accompany polyploidy in plants.
The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, ...oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition GTs also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial GTs show a higher sequence similarity in comparison to mammalian ones. Even when most GTs are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial GTs, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.
In holometabolous insects, the immature or larval stage is characterized by a high rate of food consumption. The nutrients obtained from which are directed towards the maintenance of metabolism, ...growth, pupation, and metamorphosis. However, when resources are scarce, the lack thereof can affect the growth rate and compromise the metamorphosis and formation of adults. Do increased energy expenditures yield outcomes similar to those resulting from restricted food intake during the larval stage? We hypothesized that removing the wax layer from the larvae of the ladybird
Cryptolaemus montrouzieri
Mulsant, 1850 would result in increased energy expenditure, which can compromise both larval growth and adult size. We compared the development time, feeding rate, and adult size of larvae with an intact wax layer, and those with constantly removed wax layers. We found that the production of the wax layer was continuous. Unlike the waxed larvae, the larvae of
C. montrouzieri
extended their development time in response to energy depletion through wax removal. The total number of mealybugs consumed by waxless larvae was higher than the total number consumed by waxed larvae; however, the daily consumption of waxless larvae was lower than that of waxed larvae. Furthermore, the adults of waxless larvae were smaller than those whose larvae had intact wax layers. This suggests that the cost associated with wax layer secretion is a pivotal factor in larval growth. Removing this layer does not get compensated by increased larval feeding or extended development time.
PCR recombination describes a process of in vitro chimera formation from non-identical templates. The key requirement of this process is the inclusion of two partially homologous templates in one ...reaction, a condition met when amplifying any locus from polyploid organisms and members of multigene families from diploid organisms. Because polyploids possess two or more divergent genomes ("homoeologues") in a common nucleus, intergenic chimeras can form during the PCR amplification of any gene. Here we report a high frequency of PCR-induced recombination for four low-copy genes from allotetraploid cotton ( Gossypium hirsutum). Amplification products from these genes ( Myb3, Myb5, G1262 and CesA1) range in length from 860 to 4,050 bp. Intergenomic recombinants were formed frequently, accounting for 23 of the 74 (31.1%) amplicons evaluated, with the frequency of recombination in individual reactions ranging from 0% to approximately 89%. Inspection of the putative recombination zones failed to reveal sequence-specific attributes that promote recombination. The high levels of observed in vitro recombination indicate that the tacit assumption of exclusive amplification of target templates may often be violated, particularly from polyploid genomes. This conclusion has profound implications for population and evolutionary genetic studies, where unrecognized artifactually recombinant molecules may bias results or alter interpretations.
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