Estimation de l’espérance de vie optimale au tournant du xxie siècle

La mesure de l’espérance de vie optimale est un exercice qui vise à estimer le nombre d’années que peut espérer vivre une population à partir des taux les plus faibles de mortalité, selon la cause, l’âge et le sexe, observés parmi les pays les plus industrialisés. Les résultats de cet exercice révèlent que l’espérance de vie optimale à la naissance, basée sur les données de 2001, serait de 87,6 ans chez les femmes et de 81,1 ans chez les hommes. En comparaison pour la même année, les valeurs d’espérance de vie à la naissance les plus élevées dans le monde industrialisé étaient enregistrées au Japon avec 85,0 ans chez les femmes et 78,1 ans chez les hommes. Au Québec, les valeurs se situaient à 82,2 ans chez les femmes et à 76,4 ans chez les hommes. Ces résultats suggèrent que des gains importants sont encore possibles en ce qui concerne la longévité moyenne des populations nationales.Optimal life expectancy measurement aims to estimate the number of years of life a population can expect, based on the lowest mortality rates by cause, age and sex observed in the most industrialised countries. The results of this exercise show that optimal life expectancy at birth, based on 2001 data, would be 87.6 years for women and 81.1 years for men. In comparison, the highest actual life expectancies at birth for the same year, recorded for Japan, are 85.0 years for women and 78.1 years for men. In Quebec these values are 82.2 years for women and 76.4 years for men. These results suggest that important gains in average longevity of national populations are still possible

Editorial: mobile elements and plant genome evolution, comparative analyzes and computational tools

Multiple changes that occur constantly in the plant genome allow an organism to develop from a single-celled embryo to a multicellular organism. A significant part of these changes is associated with the recombination activity of numerous classes of interspersed repeats. These numerous families of interspersed repeats were often called "junk DNA" as they were not associated with vital protein-coding processes (1). Transposable elements (TEs), such as DNA transposons and retrotransposons, are the main part of these interspersed repeats (2). DNA transposons can rightfully be called true mobile elements, the activity of which can occur at any stage of cell development and manifest itself at any moment and stage of the organism's development. The diverse families of retrotransposons are highly abundant genetic elements that are related to retroviruses (3). Although retrotransposons are not true mobile elements like DNA transposons, retrotransposable elements (RTEs) form a variety of chromosomal structures, such as centromeric and telomeric regions (4), and are the main intergenic part of the genome (5). Retrotransposons move to new chromosomal locations via an RNA intermediate that is converted into extrachromosomal DNA by the encoded reverse transcriptase/RNaseH enzymes prior to reinsertion into the genome. This replicative mode of transposition can rapidly increase the copy number of elements and can thereby greatly increase plant genome size. RTEs can be clustered into distinct families each traceable to a single ancestral sequence or a closely related group of ancestral sequences. In contrast to multigene families, which are defined based on their biological role, repetitive families are usually defined based on their active ancestors (called master or source genes) and on their generation mechanisms. Over time, individual elements from repetitive families may acquire diverse biological roles. Some RTEs can provide evolutionary advantages to the host and increase their chances of survival (6). While the view that RTEs are beneficial to the host is not new, recent progress in the field has placed RTEs squarely in the center of the ongoing debate on eukaryotic evolution. To advance this important research field, in the Research Topic "Mobile Elements and Plant Genome Evolution, Comparative Analyses, and Computational Tools" we focus on the role of mobile elements with host genome evolution, discovery, and comparative and genome-wide profiling analysis of transposable elements. Different retrotransposon families, each with its own lineage and structure, may have been active at distinct phases in the evolution of a species. Retrotransposon sequences bear the promoters that bind the nuclear factors of transcription initialization and initiate RNA synthesis by polymerases II or III. In the article entitled "Additional ORFs in Plant LTR-Retrotransposons" by Vicient C.M. and Casacuberta J.M., LTR-retrotransposons that carry additional, not retrotransposon-specific open reading frames (aORF), were discovered and analyzed. This discovery expands on the unique potential of LTR-retrotransposons as evolutionary tools, as LTR-retrotransposons can be used to deliver new gene variants within a genome. The presence of a unique aORF in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, are just as typical as retrovirus gene transduction. As dispersed and ubiquitous mobile elements, the life cycle of replicative transposition leads to genome rearrangements that affect cellular function (7). Transposable elements are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. The research group led by Kashkush K., reported the potential impact of miniature transposable element insertions on the expression of wheat genes in different wheat species in the articles entitled "The Evolutionary Dynamics of a Novel Miniature Transposable Element in the Wheat Genome" and "Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome". The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, which leads to "genomic stress" (8). TEmediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. TEs also contribute to genome plasticity and have a dramatic impact on the genetic diversity and evolution of the wheat genome. Using transposon display (9) and genome-wide profiling analysis of insertional polymorphisms of transposable elements (10), the authors discovered large genomic rearrangement events, such as deletions and introgressions in the wheat genome. High-throughput bioinformatics with next-generation sequencing (NGS) were key tools in these studies (11). Chromosomal rearrangements, gene duplications, and transposable element content may have a large impact on genomic structure, which could generate new phenotypic traits (7). In the article entitled "Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa", de Carvalho J.F. et al investigated structural variants and repetitive content between two accessions of Brassica rapa genomes and genome-size variation among a core collection using comparative genomics and cytogenetic approaches. Large genomic variants with a chromosome length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu' belonging to different cultigroups of B. rapa highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability. Transposable elements are also the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic instability and evolution. Remnants of RTEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation. RTEs are dynamic and play a role in chromosome crossing over recognition and in DNA recombination between homologous chromosomes. In the article entitled "Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding", Wang X. et al revealed that post-polyploidization of cotton genome instability resulted in numerous genomic structural changes, DNA inversion and translocation, illegitimate recombinations, accumulation of repetitive sequences, and functional innovation accompanied by elevated evolutionary rates of genes. This genome study also revealed the evolutionary past of cotton plants, which were recursively affected by polyploidization, with a decaploidization contributing to the formation of the genus Gossypium, and a neo-tetraploidization contributing to the formation of the currently widely cultivated cotton plants. The centromere is a unique part of the chromosome that combines a conserved function with extreme variability in its DNA sequence. In the article entitled "Functional Allium fistulosum centromeres comprise arrays of a long satellite repeat, insertions of retrotransposons and chloroplast DNA" Kirov G.I., et al studied the largest plant genomic organization of the functional centromere in large-sized chromosomes in Allium fistulosum and A. cepa. Long, high-copy repeats are associated with insertions of retrotransposons and plastidial DNA, and the landscape of the centromeric regions of these species possess insertions of plastidial DNA. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution. As such, the Spinacia genus serves as an ideal model to investigate the evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. This was studied in the article entitled "Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution" by Li N., et al. Major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative, sugar beet, were elucidated in the evolutionary processes of sex chromosome evolution using NGS data. The differences of repetitive DNA sequences correlate with the formation of sex chromosomes and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes, as heteromorphic sex chromosomes existed exclusively in Spinacia tetrandra.Non peer reviewe

Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization

BACKGROUND: Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values) in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation) in synthetic B. napus. RESULTS: The complete set of non-additive proteins (335 in the stem and 205 in the root), as well as a subset of additive polypeptides (200 per organ), was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55%) displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under-represented among the proteins displaying non-additive values in the allopolyploids. CONCLUSION: Protein identification showed that functionally related polypeptides (isoforms and complex subunits) could be differentially regulated in synthetic B. napus in comparison to its diploid progenitors while such proteins are usually expected to display co-regulation. The genetic redundancy within an allopolyploid could explain why functionally related proteins could display imbalanced levels of expression. No functional category, no metabolic pathway and no subcellular localization was found to be over- or under-represented within non-additive polypeptides, suggesting that the differential regulation of gene products was not related to functional properties of the proteins. Thus, at the protein level, there is no evidence for the "genomic shock" expected in neo-polyploids and the overall topology of protein networks and metabolic pathways is conserved in synthetic allotetraploids of B. napus in comparison to its diploid progenitors B. rapa and B. oleracea

Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. (Résumé d'auteur

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Les séquences répétées de la canne à sucre : spécificités génomiques et apport aux programmes d'introgression

La canne à sucre est une espèce majeure des zones tropicales, où elle est cultivée essentiellement pour sa production de sucre. Les variétés modernes de canne ont une origine interspécifique n'impliquant que quelques clones de la canne noble Saccharum officinarum et de l'espèce sauvage S. spontaneum. Face au ralentissement du progrès génétique constaté dans les années 60, les sélectionneurs ont mis en place de nouveaux programmes d'introgression impliquant d'autres espèces et genres sauvages apparentés a la canne à sucre (complexe Saccharum), afin d'augmenter la variabilité génétique. Jusqu'à présent, ces programmes n'ont connu qu'un succès limité, notamment du fait du manque de connaissances sur la différenciation des génomes nécessaire pour une meilleure maîtrise des mécanismes d'introgression. La difficulté à repérer, à l'aide des seuls caractères morphologiques, les hybrides intergénériques représente la première contrainte que rencontrent ces programmes. Nous avons exploité les caractéristiques propres des séquences d'ADN répétées présentes au sein du complexe Saccharum pour étudier la différenciation des génomes en présence et développer des outils diagnostics d'aide à la sélection. En effet, soumises à une dynamique évolutive originale, certaines de ces séquences sont spécifiques d'espèce et constituent des marqueurs moléculaires utiles en analyse phylogénétique et suivi d'introgression. Plusieurs types de séquences répétées ont été isolés, caractérises et/ou exploités : ADN satellites subtélomériques, ADN satellites centromériques, ADN ribosomaux, séquences de type inter-Alu, rétrotransposons. La différenciation des génomes des espèces comparées a été la plus forte pour les séquences en tandem des régions subtélomériques et les séquences de type inter-Alu. Dans le premier cas, des séquences spécifiques d'Erianthus et de S. officinarum / S. robustum ont été isolées. Dans le second cas, il s'agit de séquences spécifiques des genres Miscanthus, Erianthus et Saccharum. L'analyse de ces différentes séquences a montré que S. officinarum et S robustum étaient des espèces très proches, et que S. spontaneum apparaissait plus éloignée. Au sein de cette dernière, a été mise en évidence une variabilité génétique importante conduisant à distinguer les clones à 2n=80 chromosomes d'Indonésie/Nouvelle Guinée et à les rapprocher de S. officinarum. Par ailleurs, il a été montré que le genre Miscanthus est plus proche génétiquement: de Saccharum que ne l'est Erianthus. La localisation physique des ADN ribosomaux 18S-5,8S-25S et 5S, par hybridation in situ, a permis de déterminer les nombres chromosomiques de base des trois espèces principales du genre Saccharum: x=8 pour S. spontaneum et x=10 pour S. officinarum et S. robustum, apportant des informations essentielles aux travaux de cartographie génétique de la canne. A partir des séquences spécifiques de genre isolées, trois tests diagnostics PCR d'analyse d'hybrides intergénériques ont été développés. Leur efficacité et leur facilité d'emploi devraient permettre la généralisation de leur utilisation dans les programmes d'introgression. (Résumé d'auteur