Search results for "genomic"

Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication.

2015

Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochon…

Throwing down a genomic gauntlet on fisheries-induced evolution

2021

Beginning with studies on crypsis and camouflage, the hypothesis that predators can generate evolutionary change in their prey has a long and rich history (1). Few predators, however, rival humans in their potential to generate selection responses and concomitant phenotypic change on contemporary timescales. In the 1930s, J. B. S. Haldane (2) mused that fishing would be an ideal candidate for such “observable evolution” within a human lifetime, proceeding “with extreme and abnormal speed.” However, it was not until the late 1970s that research on fisheries-induced evolution (FIE) gained a substantive scientific foothold, beginning with thought-provoking work on Canadian whitefish ( Coregonu…

Plant stress biology in epigenomic era.

2020

Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanis…

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

2017

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute…

Covariation and phenotypic integration in chemical communication displays: biosynthetic constraints and eco-evolutionary implications

2018

Chemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking. We assessed the phenotypic integration of CCDs in a meta‐analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules. Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated t…

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

2017

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and th…

A self-inducible heterologous protein expression system in Escherichia coli

2016

AbstractEscherichia coli is an important experimental, medical and industrial cell factory for recombinant protein production. The inducible lac promoter is one of the most commonly used promoters for heterologous protein expression in E. coli. Isopropyl-β-D-thiogalactoside (IPTG) is currently the most efficient molecular inducer for regulating this promoter’s transcriptional activity. However, limitations have been observed in large-scale and microplate production, including toxicity, cost and culture monitoring. Here, we report the novel SILEX (Self-InducibLe Expression) system, which is a convenient, cost-effective alternative that does not require cell density monitoring or IPTG inducti…

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

2017

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine …

A roadmap for understanding the evolutionary significance of structural genomic variation

2020

Author's accepted manuscript Structural genomic variants (SVs) take diverse forms and are ubiquitous drivers of ecological and evolutionary processes. Most studies of SVs focus on the adaptive significance of gene duplications and large inversions. Future studies should catalog SVs of all types and sizes and systematically test their evolutionary implications. We propose a roadmap and definitions for the study of SVs in ecological and evolutionary genomics. Best practices for SV detection are needed to facilitate comparisons across studies. Integrating population genomic, theoretical, and experimental approaches to SVs will more comprehensively characterize genomic variation, uncover the ad…

2017

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; M…