MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts (...) decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and (...) others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Plant genome editing has the potential to become another chapter in the intractable debate that has dogged agricultural biotechnology. In 2016, 107 Nobel Laureates accused Greenpeace of emotional and dogmatic campaigning against agricultural biotechnology and called for governments to defy such campaigning. The Laureates invoke the authority of science to argue that Greenpeace is putting lives at risk by opposing agricultural biotechnology and Golden Rice and is notable in framing Greenpeace as unethical and its views as marginal. This paper (...) examines environmental, food and farming NGOs’ social and ethical concerns about genome editing, situating these concerns in comparison to alternative ethical assessments provided by the Nuffield Council on Bioethics, a key actor in this policy debate. In doing so, we show that participant NGOs and the Nuffield Council on Bioethics share considerable concerns about the social and ethical implications of genome editing. These concerns include choices over problem/solution framing and broader terminology, implications of regulatory and research choices on consumer choice and relations of power. However, GM-engaged NGOs and the Nuffield Council on Bioethics diverge on one important area: the NGOs seek to challenge the existing order and broaden the scope of debate to include deeply political questions regarding agricultural and technological choices. This distinction between the ethical positions means that NGOs provide valuable ethical insight and a useful lens to open up debate and discussion on the role of emerging technologies, such as genome editing, and the future of agriculture and food sovereignty. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

In discussions on genetic engineering and plant breeding, the intrinsic value of plants and crops is used as an argument against this technology. This paper focuses on the new field of plant genomics, which, according to some, is almost the same as genetic engineering. This raises the question whether the intrinsic value of plants could also be used as an argument against plant genomics. We will discuss three reasons why plant genomics could violate (...) the intrinsic value of plants: 1. genomics is part of biotechnology; 2. genomics equals genetic engineering; 3. plant genomics may enhance trends that lead to the instrumentalization of plants. We will conclude that in the biotic view the intrinsic value of plants is violated by plant genomics only in case of 'the genomics equals genetic engineering scenario'. (shrink)

The variation in genome size and basic chromosome number was analyzed in the wide range of angiosperm plants. A divergence of monocots vs. dicots (eudicots) genome size distributions was revealed. A similar divergence was found for annual vs. perennial dicots. The divergence of monocots vs. dicots genome size distributions holds at different taxonomic levels and is more pronounced for species with larger genomes. Using nested analysis of variance, it was shown that putative constraints on genome size variation are not only (...) stronger in dicots as compared to monocots but in the former they start to operate already at the family level, whereas in the latter they do so only at the order level. At the same time, variation in basic chromosome number is constrained at the order level in both groups. Higher basic chromosome numbers were found in perennial plants as compared to the annual ones, which can be explained by their need for a higher genetic recombination as compensation for the longer life-cycles. A negative correlation was found between genome size and basic chromosome number, which can be explained as a trade-off between different recombination mechanisms. (shrink)

Despite the enormous diversity in plant form, structure and growth environment across the seed‐bearing plants (angiosperms and gymnosperms), the chloroplast genome has, with few exceptions, remained remarkably conserved. This conservation suggests the existence of universal evolutionary selection pressures associated with photosynthesis—the primary function of chloroplasts. The stark exceptions to this conservation occur in parasitic angiosperms, which have escaped the dominant model by evolving the capacity to obtain some or all of their carbon (and nutrients) from their plant hosts. (...) The consequence of this evolution to parasitism is a relaxation of the evolutionary constraints associated with the need to maintain photosynthetic function, the very function that drove early stages of the ancient symbiotic relationship that produced the contemporary chloroplast. Extreme examples of reductionism among parasitic angiosperms reveals major alterations in chloroplast function with the loss of photosynthetic capacity and, with that, massive alterations in chloroplast genome content. This review highlights emerging patterns in reported gene loss and gene retention in the chloroplast genomes of parasitic plants. Some gene losses appear to occur in the early stages of parasitic evolution, even before the loss of photosynthetic capacity, like the chlororespiratory (ndh) genes. This contrasts with unexpected gene retentions, like that of the rbcL gene responsible for photosynthetic carbon dioxide fixation, and belies current understanding of gene function. The review relates gene retention to current knowledge of protein function and gene processing that has implications to broader aspects of genome conservation in organelles. BioEssays 26:235–247, 2004. Wiley Periodicals, Inc. (shrink)

Plastids and mitochondria arose through endosymbiotic acquisition of formerly free-living bacteria. During more than a billion years of subsequent concerted evolution, the three genomes of plant cells have undergone dramatic structural changes to optimize the expression of the compartmentalized genetic material and to fine-tune the communication between the nucleus and the organelles. The chimeric composition of many multiprotein complexes in plastids and mitochondria (one part of the subunits being nuclear encoded and another one being encoded in the organellar genome) (...) provides a paradigm for co-evolution at the cellular level. In this paper, we discuss the co-evolution of nuclear and organellar genomes in the context of environmental adaptation in species and populations. We highlight emerging genetic model systems and new experimental approaches that are particularly suitable to elucidate the molecular basis of co-adaptation processes and describe how nuclear-cytoplasmic co-evolution can cause genetic incompatibilities that contribute to the establishment of hybridization barriers, ultimately leading to the formation of new species. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth (...) and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for (...) all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Current models for regulation of parent‐specific gene expression in plants have been based on a small number of imprinted genes in Arabidopsis. These present repression as the default state, with expression requiring targeted activation. In general, repression is associated with maintenance methylation of cytosines, while no role has been found in Arabidopsis imprinting for de novo methylation—unlike the case in mammals. A recent paper1 both reinforces and challenges the model drawn from Arabidopsis. Methylation patterns of two imprinted loci in maize (...) were tracked from gametes to offspring, enabling an exploration of the timing of imprinting. For one gene, fie1, the results were as expected: parent‐specific methylation patterns were inherited from the three types of gamete: egg, central cell and sperm. The behaviour of fie2, however, was a surprise: no alleles were methylated in the gametes, although paternally contributed fie2 is methylated and silent in the endosperm, indicating that, in some cases, plant imprinting requires de novo DNA methylation. This work significantly broadens our understanding of plant imprinting and points to a greater diversity in imprinting mechanisms than has previously been appreciated. BioEssays 28: 1167–1171, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator‐like effector proteins, which are easier to engineer to target new DNA sequences than the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)‐associated protein (Cas) system (clustered regularly interspaced short palindromic (...) sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR‐Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human pathways or to improve key organisms for biotechnological applications, such as plants, livestock genome as well as yeasts and bacterial strains. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to (...) class='Hi'>plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Traditionally, plant viruses are viewed as harmful, undesirable pathogens. However, their genomes can provide several useful ‘designer functions’ or ‘sequence modules’ with which to tailor future gene vectors for plant or general biotechnology.The majority (77 %) of known plant viruses have single‐stranded RNA of the messenger (protein coding) sense as their genetic material. Over the past 4 years, improved in vitro transcription systems and the construction of partial of fulllength DNA copies of several plant RNA viruses (...) have enhanced our ability to manipulate and study their genomes, particularly in the context of their pathogenic interactions with host plants.Recently, two forms of genetically engineered protection against plant virus infections have been reported. In both, a virus‐related ‘interfering’ molecule was stably introduced into plants via the DNA‐transfer mechanism of Agro‐bacterium tumefaciens. To date, the choice of ‘interfering’ molecule has been guided by empirical field‐observations and each is effective against only a narrow range of closely‐related viruses. As yet, we do not fully understand the molecular mechanism(s) responsible for the observed protection.The ability to manipulate the plant–pathogen relationship is a powerful tool to increase our knowledge and improve future strategies for uncoventional cropprotection by genetic engineering techniques. (shrink)

Genes are functional cell segments of DNA within an organism, as well as basic physical units of biological inheritance, which have consequences for human dignity and public interest. Genes and genetic material (DNA strands of nucleotides, genetically altered plants and animals e.g., see Appendix B) are patentable. In the US and around the globe, governments grant genetic patents for new, non-obvious, and useful gene inventions. A wide range of interest groups such as religious leaders, scientists, biotech pharmaceuticals, medical practitioners, health (...) care providers, venture capitalists, medical patients and persons have interests in defining what is subject to patents. Yet, it is at least questionable that genetic inventions, and the ownership of discoveries of gene mutations leading to possible diseases, should be subject to influence by interest groups. Although some genes (cDNA) are currently legally patentable, the question in this examination is whether gene patents should be legally and morally justified. In this work I examine whether gene patents should legally and morally be justified, given the principles of biomedical ethics such as human Beneficence /Autonomy and Justice. I argue that gene patenting is not justifiable, and I consider what can be done to create a system that delivers access to genetic information in the current genetic Intellectual Patent system. This interdisciplinary work is more complex than whether bio-science researchers and corporate entities should hold gene patents, or differentiating the legal question of whether genes are an invention or a discovery in the human genome. Mere responses to these questions would not ultimately solve the genetic justice problem. The justification for genetic appropriation is more complexity, since it is grounded in axiological claims about human dignity and public interest set in an ever changing biomedical/biogenetic technology. To address this complexity, I will draw upon the ideas of “the capability approach” to genetic justice found in the work of Nussbaum and Sen. This work is an interdisciplinary examination of the proper appropriation of natural genetic material and its impact on human dignity. It is argued that genetic material and information should be accessible to all, via heath care, for example. We must look to new ways to achieve genetic justice that promote human flourishing as a public good. (shrink)

Genebanking, the process of preserving genetic resources, is a central practice in the modern management of crop genetics, especially for the species used for food and agriculture. Closely interrelated networks of local, national and global actors are responsible for ex situ conservation. They all seek to make plant genetic resources accessible for all and now face new challenges arising from digitisation. Plant sciences are entering the postgenomic era, moving fast from initially providing a single reference genome for each (...) species (genomics), to harnessing the extent of diversity within crop species (pangenomics) and among their relatives (referred to as postgenomics). This paper describes the extent to which ex situ collections have already undergone a digital shift, or are planning to do so, and the potential impact of this postgenomic-induced dematerialisation on the global governance of plant genetic resources. In turn, digitising material (seed) collection changes the relationship between genebanks and genomic databases. Comprehensive genomic characterisation of genebank accessions is ongoing, and I argue here that these efforts may provide a unique opportunity for genebanks to further embrace the moral, ethical and ultimately political principles on which they were built. Repurposing genebanks as decentralised digital biocentres could help relocate capabilities and stewardship over genetic resources. Empowering local farmers by providing access, promoting the use and unlocking benefits from state-of-the-art tools of modern plant breeding may allow bridging the breeding divide. However, to accomplish such a paradigm shift, genebanks require a strong political mandate that must primarily originate from the access and benefit-sharing framework. Only so may the global challenges associated with the loss of biodiversity and food insecurity be addressed. (shrink)

Public opinion can affect the adoption of genome editing technologies. In food production, genome editing can be applied to a wide range of applications, in different species and with different purposes. This study analyzed how the public responds to five different applications of genome editing, varying the species involved and the proposed purpose of the modification. Three of the applications described the introduction of disease resistance within different species, and two targeted product quality and quantity in cattle. Online surveys in (...) Canada, the US, Austria, Germany and Italy were carried out with a total sample size of 3698 participants. Using a between-subject design, participants were confronted with one of the five applications and asked to decide whether they considered it right or wrong. Perceived risks, benefits, and the perception of the technology as tampering with nature were surveyed and were complemented with socio-demographics and a measure of the participants’ moral foundations. In all countries, participants evaluated the application of disease resistance in humans as most right to do, followed by disease resistance in plants, and then in animals, and considered changes in product quality and quantity in cattle as least right to do. However, US and Italian participants were generally more positive toward all scenarios, and German and Austrian participants more negative. Cluster analyses identified four groups of participants: ‘strong supporters’ who saw only benefits and little risks, ‘slight supporters’ who perceived risks and valued benefits, ‘neutrals’ who showed no pronounced opinion, and ‘opponents’ who perceived higher risks and lower benefits. This research contributes to understanding public response to applications of genome editing, revealing differences that can help guide decisions related to adoption of these technologies. (shrink)

This chapter argues for the importance of considering conceptual and normative commitments when addressing questions of responsible practice in data-intensive agricultural research and development. We consider genetic gain-focused plant breeding strategies that envision a data-intensive mode of breeding in which genomic, environmental and socio-economic data are mobilised for rapid crop variety development. Focusing on socio-economic data linkage, we examine methods of product profiling and how they accommodate gendered dimensions of breeding in the field. Through a comparison with participatory breeding (...) methods, we argue that the conceptual commitments underpinning current methods of integrating socioeconomic data into calculations of genetic gain can preclude the achievement of key social development goals, and that better engagement with participatory approaches can help address this problem. We conclude by identifying three key avenues towards a data-intensive approach to plant breeding that utilises the diverse sources of relevant evidence available, including socio-economic data, and maximises the chance of developing sustainable and responsible strategies and research practices in this domain: (1) reliable, long-term management of data infrastructures; (2) ongoing critical analysis of the conceptual foundations of specific strategies; and (3) regular transdisciplinary consultations including expertise in the social studies of agricultural science as well as participatory breeding techniques. (shrink)

Clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR‐associated protein (CRISPR/Cas) system has revolutionized genetic research in the life sciences. Four classes of CRISPR/Cas‐derived genome editing agents, such as nuclease, base editor, recombinase, and prime editor have been introduced for engineering the genomes of diverse organisms. The recently introduced prime editing system offers precise editing without many off‐target effects than traditional CRISPR‐based systems. Many researchers have successfully applied this gene‐editing toolbox in diverse systems for various genome‐editing applications. This review presents the mechanism (...) of prime editing and summarizes the details of the prime editing system applied in plants and mammalian cells for precise genome editing. We also discuss the advantages, limitations, and potential future applications of prime editing in these systems. This review enables the researcher to gain knowledge on prime editing tools and their potential applications in plants and mammalian cells. (shrink)

Two groups of plant viruses have DNA in their genomes. One group, the caulimoviruses, are non‐integrating retroviruses that package dsDNA in virions. The other group, the geminiviruses, package small circular ssDNA and include the only DNA viruses known with bipartite genomes. The regulation of transcription of these viruses is not well characterized, but recent work is beginning to yield interesting results. Regulatory sequences from these viruses function in cells of species that are not hosts of the virus and are (...) finding use in constitutive expression of chimeric genes in transformed plants. Development of vectors based on plant viruses requires further characterization at the molecular level of viral life cycles. (shrink)

First uniform description of all key levels of communication in the organismic kingdoms of plants, fungi, animals (bees and corals), bacteria and additionally the natural genome editing competences of viruses based on the most recent empirical data. The biocommunicative approach presented is based on the results of the philosophy of science discourse concerning coherent definitions of 'language' and 'communication'.

Arabidopsis thaliana (Thale cress, Arabidopsis) is an ideal model organism for the molecular genetic analysis of many plant processes. The availability of a complete physical map would greatly facilitate the gene cloning steps in these studies. The small genome size of Arabidopsis makes the construction of such a map a feasible goal. One of the approaches to construct an overlapping library of the Arabidopsis genome takes advantage of the many mapped markers and the availability of Arabidopsis yeast artificial chromosome (...) (YAC) libraries. Mapped molecular markers are used to identify corresponding YAC clones and thereby place them on the genetic map. Subsequently, these YAC clones provide the framework for directed walking experiments aimed at closing the gaps between the YAC contigs. Adopting this strategy, YAC clones comprising about 10% of the genome have been assigned to the top halves of Arabidopsis chromosomes 4 and 5. Extensive walking experiments in a 10 cM interval of chromosome 4 have resulted in two contiguous regions in the megabase size range. (shrink)

This book inquires into the swarm of ontological, epistemological, and ethical questions provoked by psychedelic experience in the context of global ecological crisis. Richard M. Doyle is professor of English and science, technology, and society at Pennsylvania State University. He is the author of On Beyond Living and Wetwares.

The unusual occurrence and developmental diversity of asexual eukaryotes remain a puzzle. De novo formation of a functioning asexual genome requires a unique assembly of sets of genes or gene states to disrupt cellular mechanisms of meiosis and gametogenesis, and to affect discrete components of sexuality and produce clonal or hemiclonal offspring. We highlight two usually overlooked but essential conditions to understand the molecular nature of clonal organisms, that is, a nonrecombinant genomic assemblage retaining modifiers of the sexual program, and (...) a complementation between altered reproductive components. These subtle conditions are the basis for physiologically viable and genetically balanced transitions between generations. Genomic and developmental evidence from asexual animals and plants indicates the lack of complementation of molecular changes in the sexual reproductive program is likely the main cause of asexuals' rarity, and can provide an explanatory frame for the developmental diversity and lability of developmental patterns in some asexuals as well as for the discordant time to extinction estimations. (shrink)

Two main attempts have been suggested for the biological significance of endopolyploidy: (i) provision of high DNA amounts to support high synthetic demands in certain cells and (ii) compensation for a lack of nuclear DNA in species with small genomes. However, in seed plants, the positive correlation between DNA content and cell volume of endopolyploid cells suggests other possibilities. Cell size paralleled by the endopolyploidy level has an impact on growth and development. Endopolyploidy levels in turn are characteristic for a (...) given species and even families, reflecting the adaptation to certain habitats during phylogeny. Furthermore, endopolyploidy levels vary to some degree between individuals of one species in response to different environmental conditions. In addition, endopolyploidy differs between different tissues suggests that a certain cell size is advantageous for a given cell function. This article reviews these findings and discusses more conclusive possible functions of endopolyploidy. BioEssays 28: 271–281, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Higher plant nuclear genomes contain many families of dispersed repeats that change during evolution. Recent evidence from studies on genetically defined transposable elements raises the possibility that many of the dispersed repeats are remnants of such elements. Transposition of DNA has also occurred between mitochondria, chloroplasts and nuclei, a fact that underlines the major role played by DNA transposition in determining the structure of plant genomes.

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression of (...) genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression of (...) genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

In the organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single‐strand‐switching or a reciprocal‐strand‐switching event. Single‐strand‐switching events lead to intermediates containing Y junctions, whereas reciprocal‐strand‐switching creates Holliday junctions. Common features in all the (...) described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements. (shrink)

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to (...) the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD defi- ciency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. (shrink)

The development of improved methods for genome‐wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k‐mers for GWAS has taken over as a new (...) thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k‐mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker‐trait associations (MTAs) that are relevant to human healthcare and crop improvement. (shrink)

Classic genetics studies found that genomic imbalance caused by changing the dosage of part of the genome (aneuploidy) has more detrimental effects than altering the dosage of the whole genome (ploidy). Previous analysis revealed global modulation of gene expression triggered by aneuploidy across various species, including maize (Zea mays), Arabidopsis, yeast, mammals, etc. Plant microRNAs (miRNAs) are a class of 20‐ to 24‐nt endogenous small noncoding RNAs that carry out post‐transcriptional gene expression regulation. That miRNAs and their putative targets (...) are preferentially retained as duplicates after whole‐genome duplication, as are many transcription factors and signaling components, indicates miRNAs are likely to be dosage‐sensitive and potentially involved in genomic balance networks. This review addresses the following questions regarding the role of miRNAs in genomic imbalance. (1) How do aneuploidy and polyploidy impact the expression of miRNAs? (2) Do miRNAs play a regulatory role in modulating the expression of their targets under genomic imbalance? (shrink)

In contrast to bilaterian animals, non‐bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature (...) suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter‐domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA. (shrink)

The use of genomic selection in agricultural animal breeding is in academic literature generally considered an ethically unproblematic development, but some critical views have been offered. Our paper shows that an important preliminary question for any ethical evaluation of genomic selection is how the scope of discussion should be set, that is, which ethical issues and perspectives ought to be considered. This scope is determined by three partly overlapping choices. The first choice is which ethical concepts to include: an ethical (...) discussion of genomic selection approaches may draw on concepts central to applied ethics, but some critical views have been based on concepts from critical animal studies and continental philosophy. A related choice is to what extent discussion should focus on new ethical issues raised or on existing ethical issues that will be ameliorated, perpetuated or aggravated by an innovation in genomic selection. The third choice is to treat an innovation in genomic selection either as a technique on itself or as a part of specific practices. We argue that ethical discussion should not limit attention to new issues or ignore the implications of particular ways of applying genomic selection in practice, and this has some consequences for which ethical concepts ought to be included. Limiting the scope of discussion may be defensible in some contexts, but broader ethical discussion remains necessary. (shrink)

Knowledge of eukaryotic life cycles and associated genome dynamics stems largely from research on animals, plants, and a small number of “model” (i.e., easily cultivable) lineages. This skewed sampling results in an underappreciation of the variability among the many microeukaryotic lineages, which represent the bulk of eukaryotic biodiversity. The range of complex nuclear transformations that exists within lineages of microbial eukaryotes challenges the textbook understanding of genome and nuclear cycles. Here, we look in‐depth at Foraminifera, an ancient (∼600 million‐year‐old) lineage (...) widely studied as proxies in paleoceanography and environmental biomonitoring. We demonstrate that Foraminifera challenge the “rules” of life cycles developed largely from studies of plants and animals. To this end, we synthesize data on foraminiferal life cycles, focusing on extensive endoreplication within individuals (i.e., single cells), the unusual nuclear process calledZerfall, and the separation of germline and somatic function into distinct nuclei (i.e., heterokaryosis). These processes highlight complexities within lineages and expand our understanding of the dynamics of eukaryotic genomes. (shrink)

During the past decade, it has become apparent that it is within our grasp to understand fully the development and functioning of complex organisms. It is widely accepted that this undertaking must include the elucidation of the genetic blueprint – the genome sequence – of a number of model organisms. As a prelude to the determination of these sequences, clonebased physical maps of the genomes of a number of multicellular animals and plants are being constructed. Yeast artificial chromosome (YAC) vectors, (...) by virtue of their relatively unbiased cloning capabilities and capacity to carry large inserts, have come to play a central role in the construction of these maps. The application of YACs to the physical map of the Caenorhabditis elegans genome has enabled cosmid clone ‘islands’ to be linked together in an efficient manner. The long‐range continuity has improved the linkage between the genetic and physical maps, greatly increasing its utility. Since the genome can be represented by a relatively small number of YACs, it has been possible to make replica filters of genomically ordered YACs available to the community at large. (shrink)

Progress in sequencing the genome of the model plant Arabidopsis is reviewed. The resulting analysis of the sequence indicates an information-rich genome that is being tackled by a variety of high-throughput approaches aimed at understanding the functions of plant genes. The information derived from these systematic studies is providing important new knowledge of biological processes found uniquely in plants for comparison with that obtained in other multicellular organisms. BioEssays 1999;21:110–120. © 1999 John Wiley & Sons, Inc.

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in (...) the regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in (...) the regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic (...) studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics. (shrink)

Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) used sequence (...) searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 Gα, 2 Gβ, 2 Gγ). C. elegans encodes one ortholog of each of the four Gα classes found in metazoans and 16 new Gα genes. The orthologous genes are widely expressed, whereas 14 of the divergent Gα genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis.BioEssays 21:713–717, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

The nucleolus is a region of the nucleus with high protein density and it acts as a ribosome factory. The nucleolus contains a distinct region of the genome, the ribosomal RNA gene repeats (rDNA) that supply ribosomal RNA (rRNA) molecules. The rDNA is the most‐abundant gene and occupies a large part of the genome, for example, there are thousands of rDNA copies in the genomes of plant cells. Therefore, it is natural to suppose that the condition of the rDNA, (...) such as its stability, might affect cellular functions. Here I would like to propose a new model regarding the roles of the rDNA and nucleolus. The key point of this model is that they act to preserve genome stability and trigger aging. BioEssays 30:267–272, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The majority of human, animal and plant viral pathogens possess genomes composed of RNA. The strategies evolved for expression and replication of viral RNA genomes can differ significantly from those utilized for expression and replication of host‐cell genetic material. Consequently, knowledge of the molecular details of these strategies can lead to a clearer understanding of the origin, evolution and control of viral pathogens. We describe recent progress in identifying important structural and functional domains of the RNA genomes and associated (...) replicative enzymes for two very different viruses: vesicular stomatitis virus, which possesses a single‐stranded RNA genome of negative polarity, and wound tumor virus, which contains a genome composed of 12 discrete segments of double‐stranded RNA. (shrink)

The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary “outpost” among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical‐zone crop. Among the goals (...) of avocado improvement are to develop varieties with fruit that will “store” better on the tree, show uniform ripening and have better post‐harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non‐flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms. BioEssays 30:386–396, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Graphical AbstractThe fungus Neurospora comprises a novel model for testing hypotheses involving the role of sex and reproduction in eukaryotic genome evolution. Its variation in reproductive mode, lack of sex-specific genotypes, availability of phylogenetic species, and young sex-regulating chromosomes make research in this genus complementary to animal and plant models.

Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) used sequence (...) searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 Gα, 2 Gβ, 2 Gγ). C. elegans encodes one ortholog of each of the four Gα classes found in metazoans and 16 new Gα genes. The orthologous genes are widely expressed, whereas 14 of the divergent Gα genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis.BioEssays 21:713–717, 1999. © 1999 John Wiley & Sons, Inc. (shrink)