Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their ...reproductive biology, water‐conducting systems, secondary metabolism, stress defense mechanisms, and small RNA‐mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole‐genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of ...individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure
entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between
and
pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in
germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of
's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.
Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we ...analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C₃–C₄ photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C₃–C₄ photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PAC-MAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.
Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution ...of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS.
Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages.
Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory.
Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups.
Le bois est un matériau renouvelable et une source d'énergie importante dont les caractéristiques physiques et chimiques sont largement définies durant sa formation et plus spécifiquement à l'étape ...de déposition de la paroi cellulaire secondaire (DPCS). Comprendre les déterminants moléculaires régissant la DPCS améliorera nos connaissances de ce processus biologique et les stratégies d'amélioration génétique du bois. Les études d'associations génétiques ont identifié de nombreux gènes impliqués dans l'étape de DPCS chez l'espèce modèle d'arbre Populus trichocarpa. Ces études n'ont pas permis d'expliquer la plupart de l'héritabilité observé pour des traits phénotypiques en utilisant seulement les variations génétiques communes. Les variations génétiques rares caractérisées par leurs faibles fréquences dans les populations sont prometteuses pour expliquer une plus grande part de l'héritabilité manquante, surtout les variants avec un effet perturbateur sur les produits géniques. Le premier chapitre de cette thèse examine la littérature scientifique sur les dernières innovations technologiques et méthodologiques basée sur la génomique qui sont utilisées pour étudier les aspects moléculaires de la formation du bois. Les avancées dans les technologies de séquençage et l'assemblage de nouveaux génomes végétaux ont permis d'élargir la gamme d'organismes disponible pour l'étude de la formation du bois. L'étude des ARN non codants et des interactions épigénétiques est devenue une partie importante de la recherche sur la régulation de l'expression des gènes impliqués dans la formation du bois. La génétique des systèmes couplée à la théorie des réseaux a été utilisée pour intégrer plusieurs couches de données moléculaires afin d'étudier la formation du bois en tant que processus biologique complexe. En termes d'amélioration du bois, la sélection basée sur la génomique a produit des résultats prometteurs par rapport aux approches de sélection traditionnelles. Les technologies de criblage à haut débit et le reséquençage rentable de génomes complets permettent désormais d'identifier les variants génétiques rares dans une population. Cependant, ces variants rares doivent être identifiées avec confiance car ils peuvent facilement être confondus avec des erreurs de séquençage. Dans le deuxième chapitre, le reséquençage de génomes entiers de P. trichocarpa a été utilisé pour identifier les petites variations génétiques rares et communes présentes chez un grand nombre d'individu. Les variations génétiques caractérisées par deux logiciels d'identification de variants ont été comparées et strictement filtrées en fonction de leur qualité. Nous avons trouvé une grande diversité génomique chez P. trichocarpa, avec 8,5 millions de petites variations génétiques. Fait important, 377 000 variations non-synonymes (5 % du total) ont été découvertes. L'importance de la diversité génomique et le potentiel des variations génétiques défectueuses rares pour expliquer une part importante de la variabilité phénotypique de P. trichocarpa sont mis en évidence. Les variations perturbatrices de l'ADN codant peuvent mener à des produits géniques défectueux et être utilisées en sélection moléculaire. Dans le troisième chapitre, 58 variations génétiques perturbatrices ont été identifiées dans les gènes de DPCS chez P. trichocarpa. Des données transcriptomiques ont ensuite été utilisées pour examiner les patrons d'expression de ces gènes. Une différence d'expression significative a été observée entre les individus avec et sans variants perturbateurs pour 13% des transcrits de gènes dans lesquels des variants perturbateurs ont été trouvés. Chez les individus hétérozygotes, l'expression spécifique de l'allèle correspondant aux variants perturbateurs et à l'allèle de référence était significativement différente pour la moitié de nos observations et variait significativement entre génotypes, clones et environnements. Le potentiel de deux variants perturbateurs dans deux gènes d'hémicellulose a été évalué pour l'amélioration du bois. Ces résultats révèlent une régulation complexe de l'expression des gènes de DPCS possédant des variations perturbatrices et soulignent l'importance des influences environnementales sur l'expression des transcrits. Cette thèse démontre l'importance de la conception des études génomiques pour l'identification des variants génétiques rares. La régulation complexe de l'expression des gènes de DPCS associée à la présence de variants perturbateurs a aussi été mise en évidence. Récemment, le domaine de la génomique du bois a connu une évolution vers une approche de plus en plus holistique pour déchiffrer la formation du bois en tant que processus biologique complexe. Les connaissances qui en résulteront amélioreront davantage nos connaissances sur les déterminants moléculaires de la formation du bois et renforceront l'efficacité des stratégies d'amélioration des arbres.
Wood is an important renewable material and energy source whose physical and chemical characteristics are mainly determined during its formation, and specifically the secondary cell wall deposition (SCWD) step. Understanding the molecular determinants of the SCWD process is thus important to improve knowledge of this biological process and wood improvement strategies. Genomics studies in the form of genetic association studies identified many genes involved in the SCWD step in the tree model species Populus trichocarpa but failed to explain most of the observed heritability in phenotypic traits using common genetic variation only. Rare genetic variants characterized by their low frequency in populations hold potential to explain more of the missing heritability, especially those variants with a disruptive effect on gene products. The first chapter of this thesis review the research literature on the latest genomics-based technological and methodological innovations used to study the molecular aspects of wood formation. Summary of these advancements highlight how breakthroughs in sequencing technologies and the availability of additional assembled and functionally annotated plant genomes have broadened the scope of organisms for investigating the distinct wood formation patterns among seed plants. The study of non-coding RNAs and epigenetic interactions has become an important part of the research on the expression regulation of genes implicated in wood formation. Systems genetics coupled with network graph theory have been used to integrate multiple layers of molecular data to study wood formation as a complex biological process. In terms of wood improvement, genomics-enabled breeding has produced similar or even better results compared to traditional selection approaches. High-throughput technologies and cost-efficient resequencing of complete genomes have enabled the identification of every genetic variation along genomes, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants, however, must be identified with high confidence, as they can easily be confounded with sequencing errors. In the second chapter, whole genome resequencing of Populus trichocarpa were used to identify rare and common small genetic variants across individual genomes. The genetic variations identified by two variant calling software were compared and filtered using strict quality criteria. Based on the variants identified by both variant callers, we found high genomic diversity in P. trichocarpa germplasm, with 8.5 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. The importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics are highlighted. Disruptive variants within coding DNA predictably leads to defective gene products and may be targets for molecular breeding. In the third chapter, 58 disruptive genetic variants were identified in P. trichcocarpa's SCWD genes, using the genetic variants recovered in Chapter 2. Two transcriptomic datasets were then used to examine the expression patterns of these genes. Transcript expression differed significantly between individuals with disruptive variants and those without in 13% of gene transcripts in which disruptive variants were found. In heterozygous individuals, the allele-specific expression of disruptive variants and the reference allele was significantly different in approximately half of our observations and varied significantly between genotypes, clonemates and environments. The potential of two disruptive variants in two hemicellulose genes, GUX and GT8D2, was also evaluated for wood improvement. Overall, these results show complex expression regulation of SCWD genes with disruptive variants and highlight the importance of environmental influences on transcript expression. This thesis demonstrates the importance of study design for the proper identification of rare genetic variants. In addition, the complex regulation of SCWD gene expression associated with the presence of disruptive variants have been highlighted. Over the past five years, the field of wood genomics has seen a shift to an increasingly holistic approach to help decipher wood formation as a complex biological process. The resulting knowledge will further improve our knowledge about the molecular determinants of wood formation and enhance the efficiency of tree breeding strategies.
Summary Substantial inequalities exist in cancer survival rates across countries. In addition to prevention of new cancers by reduction of risk factors, strategies are needed to close the gap between ...developed and developing countries in cancer survival and the effects of the disease on human suffering. We challenge the public health community's assumption that cancers will remain untreated in poor countries, and note the analogy to similarly unfounded arguments from more than a decade ago against provision of HIV treatment. In resource-constrained countries without specialised services, experience has shown that much can be done to prevent and treat cancer by deployment of primary and secondary caregivers, use of off-patent drugs, and application of regional and global mechanisms for financing and procurement. Furthermore, several middle-income countries have included cancer treatment in national health insurance coverage with a focus on people living in poverty. These strategies can reduce costs, increase access to health services, and strengthen health systems to meet the challenge of cancer and other diseases. In 2009, we formed the Global Task Force on Expanded Access to Cancer Care and Control in Developing Countries, which is composed of leaders from the global health and cancer care communities, and is dedicated to proposal, implementation, and evaluation of strategies to advance this agenda.
•Tonal variability impacts Cantonese and French toddlers’ word-learning.•Cantonese- and French-speaking adults remain partly sensitive to tone variation.•Tonal interference in word-learning is not ...specific to tone-language-learners.•Tonal interference is likely phonological in Cantonese and acoustic in French.•Toddlers can learn novel words in an unfamiliar language after brief exposure.
Most languages of the world use lexical tones to contrast words. Thus, understanding how individuals process tones when learning new words is fundamental for a better understanding of the mechanisms underlying word learning. The current study asked how tonal information is integrated during word learning. We investigated whether variability in tonal information during learning can interfere with the learning of new words and whether this is language and age dependent. Cantonese- and French-learning 30-month-olds (N = 97) and Cantonese- and French-speaking adults (N = 50) were tested with an eye-tracking task on their ability to learn phonetically different pairs of novel words in two learning conditions: a 1-tone condition in which each object was named with a single label and a 3-tone condition in which each object was named with three different labels varying in tone. We predicted learning in all groups in the 1-tone condition. For the 3-tone condition, because tones are part of the phonological system of Cantonese but not of French, we expected the Cantonese groups to either fail (toddlers) or show lower performance than in the 1-tone condition (adults), whereas the French groups might show less sensitivity to this manipulation. The results show that all participants learned in the 1-tone condition and were sensitive to tone variation to some extent. Learning in the 3-tone condition was impeded in both groups of toddlers. We argue that tonal interference in word learning likely comes from the phonological level in the Cantonese groups and from the acoustic level in the French groups.
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