La flore du conservatoire botanique Michel Adanson de Mbour (Sénégal): perspective pour un plan d’aménagement et de gestion

Objectif: Cette étude a été réalisée dans la commune de Mbour dans le but de caractériser la flore du conservatoire botanique Michel ADANSON. Elle se propose d’établir la composition spécifique, les spectres taxonomique, biologique et chorologique et d’apprécier la fréquence et l’abondance des espèces.Méthodologie et résultats: Des relevés phytosociologiques ont été réalisées en 2010 dans le conservatoire. Au total 140 espèces ont été recensées, réparties dans 115 genres et 53 familles. Les Dicotylédones représentent 90,57% des espèces de la flore contre 9,43% de Monocotylédones. La plupart des espèces sont des nanophanerophytes (47,86%) et des thérophytes (47,86%). Cette flore est aussi marquée par la prédominance des espèces africaines (33,8%) et des espèces pantropicales (21,6%).Plus de la moitié des espèces (59%) recensées sont rares ou accidentelles du fait du caractère du site qui est un conservatoire. Environ 7,86% des espèces du conservatoire sont qualifiées d’espèces constantes. Nous avons 2,26% des espèces qui ont un recouvrement moyen de 32%, ces espèces sont les plus abondantes du conservatoire.Conclusion et application: Ce travail a permis de déterminer la structure du conservatoire botanique Michel ADANSON de Mbour. En effet, les spectres taxonomique, botanique, et chorologique sont déterminés de même que la fréquence des espèces et leur abondance dominance. Ces résultats sont importants pour la mise en place d’un plan d’aménagement et de gestion du conservatoire.Mots clés: flore, végétation, Conservatoire botanique, ENDA, MbourEnglish Title: The flora of the Michel Adanson botanical conservatory Mbour (Senegal): perspective for management and developmentEnglish AbstractObjective: This study was conducted in the town of Mbour in order to characterize the flora of the botanical conservatory Michel Adanson. It proposes to establish the species composition, the taxonomic spectra, biological and chorological and appreciate the frequency and abundance of species.Methodology and Results: Phytosociological surveys were conducted in 2010 in the conservatory. In total 140 species were recorded, distributed in 115 genera and 53 families. Dicotyledons represent 90.57% of the species of flora against 9.43% of Monocotyledons. Most species are nanophanerophytes (47.86%) and therophytes (47.86%). This flora is also marked by the predominance of African species (33.8%) and pantropical species (21.6%). More than half of the species (59%) surveyed are rare or accidental because of the character of the site which is a conservatory. Approximately 7.86% of the conservatory species are referred to constant species. There are 2.26% of the species that have an average recovery of 32%, those species are the most abundant of the conservatory.Conclusion and Application: This work has determined the structure of the botanical conservatory Michel Adanson Mbour. Indeed, the taxonomic spectra, botany, and chorological are determined as well as the frequency and abundance of species dominance. These results are important for the establishment of a management plan and interim management.Keywords: flora, vegetation, Botanical Conservatory, ENDA, Mbou

The transcriptome of metamorphosing flatfish

Background Flatfish metamorphosis denotes the extraordinary transformation of a symmetric pelagic larva into an asymmetric benthic juvenile. Metamorphosis in vertebrates is driven by thyroid hormones (THs), but how they orchestrate the cellular, morphological and functional modifications associated with maturation to juvenile/adult states in flatfish is an enigma. Since THs act via thyroid receptors that are ligand activated transcription factors, we hypothesized that the maturation of tissues during metamorphosis should be preceded by significant modifications in the transcriptome. Targeting the unique metamorphosis of flatfish and taking advantage of the large size of Atlantic halibut (Hippoglossus hippoglossus) larvae, we determined the molecular basis of TH action using RNA sequencing. Results De novo assembly of sequences for larval head, skin and gastrointestinal tract (GI-tract) yielded 90,676, 65,530 and 38,426 contigs, respectively. More than 57 % of the assembled sequences were successfully annotated using a multi-step Blast approach. A unique set of biological processes and candidate genes were identified specifically associated with changes in morphology and function of the head, skin and GI-tract. Transcriptome dynamics during metamorphosis were mapped with SOLiD sequencing of whole larvae and revealed greater than 8,000 differentially expressed (DE) genes significantly (p < 0.05) up- or down-regulated in comparison with the juvenile stage. Candidate transcripts quantified by SOLiD and qPCR analysis were significantly (r = 0.843; p < 0.05) correlated. The majority (98 %) of DE genes during metamorphosis were not TH-responsive. TH-responsive transcripts clustered into 6 groups based on their expression pattern during metamorphosis and the majority of the 145 DE TH-responsive genes were down-regulated. Conclusions A transcriptome resource has been generated for metamorphosing Atlantic halibut and over 8,000 DE transcripts per stage were identified. Unique sets of biological processes and candidate genes were associated with changes in the head, skin and GI-tract during metamorphosis. A small proportion of DE transcripts were TH-responsive, suggesting that they trigger gene networks, signalling cascades and transcription factors, leading to the overt changes in tissue occurring during metamorphosis

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

El\ue9ments de pr\ue9cision des aires de distribution du fonio et de ses apparent\ue9s sauvages en fonction des zones climatiques, des types de v\ue9g\ue9tation et de sols au S\ue9n\ue9gal

White fonio ( Digitaria exilis Stapf) is one of the most promising cereals in West Africa due to its nutritional qualities and for its potential to generate financial returns for women. In Senegal, its culture has declined in recent years as well as the distribution area of its wild relatives. This study aims to specify the ecology of wild relatives of fonio. The data used come from collections of DAKAR and IFAN Herbaria, the GBIF database and field collections which made it possible to draw species distribution maps according to the climatic zones, vegetation and soils types. The results of the study revealed that the Sudanian zone is the richest in term of specific diversity with 11 inventoried species. The species occupy all types of vegetation in Senegal and the presence of some in arid zones, steppe type, and wet zones composed mainly of forests and wooded savannahs attests their remarkable adaptation to contrasting environmental conditions. It is also apparent from this study that species prefer tropical ferruginous soils, lithosols, ferralitic and hydromorphic soils. Digitaria ciliaris and D. gayana occur on almost all types of soils. As for D. exilis, it grows on the same soil as D. longiflora , its closest wild relative. The development of seed banks for the ex situ conservation of these wild species, potential sources of genes for fonio, would be of primary importance for the protection of this biodiversity.Le fonio blanc ( Digitaria exilis Stapf) est l\u2019une des c\ue9r\ue9ales les plus prometteurs en Afrique de l\u2019Ouest gr\ue2ce \ue0 ses qualit\ue9s nutritionnelles et de g\ue9n\ue9ration de revenus par les femmes. Au S\ue9n\ue9gal, sa culture a r\ue9gress\ue9 ces derni\ue8res ann\ue9es de m\ueame que l\u2019aire de r\ue9partition de ses parents sauvages. Cette \ue9tude vise ainsi \ue0 pr\ue9ciser l\u2019\ue9cologie des apparent\ue9es sauvages du fonio. Les donn\ue9es utilis\ue9es proviennent de collections des Herbiers DAKAR et IFAN, de la base de donn\ue9es GBIF et de collectes de terrain qui ont permis de dessiner des cartes de r\ue9partition des esp\ue8ces en fonction des zones climatiques, des types de v\ue9g\ue9tation et de sols. Les r\ue9sultats de l\u2019\ue9tude ont r\ue9v\ue9l\ue9 que la zone soudanienne est la plus riche en termes de diversit\ue9 sp\ue9cifique avec 11 esp\ue8ces inventori\ue9es. Les esp\ue8ces occupent tous les types de v\ue9g\ue9tation du S\ue9n\ue9gal et la pr\ue9sence de certaines en zones arides, de type steppe, et humides compos\ue9es principalement de for\ueats et de savanes bois\ue9es t\ue9moigne leur remarquable adaptation \ue0 des conditions environnementales contrast\ue9es. Il ressort \ue9galement de cette \ue9tude que les esp\ue8ces affectionnent mieux les sols ferrugineux tropicaux, les lithosols, les sols ferralitiques et hydromorphes. Digitaria ciliaris et D. gayana se rencontrent sur presque l\u2019ensemble des types de sols. Quant \ue0 D. exilis, elle pousse sur les m\ueames sols que D. longiflora , son plus proche parent sauvage. Le d\ue9veloppement de banques de semences assurant la conservation ex situ de ces esp\ue8ces sauvages, sources potentielles de g\ue8nes pour le fonio, serait d\u2019une importance primordiale pour la sauvegarde de cette biodiversit\ue9

DNA-sequencing-based assessment of seaweed biodiversity and distribution along the Senegalese coast

International audienc

DNA-sequencing-based assessment of seaweed biodiversity and distribution along the Senegalese coast

International audienc

Caractérisation de la flore phytoplanctonique dans l'Aire Marine Protégée (AMP) de Bamboung et de deux sites environnants (Sénégal)

Au Sénégal, peu d'études sur le plan planctonique ont été réalisées pour l'évaluation de l'efficacité des Aires Marines Protégées. Dans cette perspective, la caractérisation de la flore phytoplanctonique et sa distribution spatio-temporelle à l'intérieur et à l'extérieur de l'AMP de Bamboung a été réalisée en avril et en septembre 2016. Des prélèvements d'échantillons d'eau à l'aide d'un filet à plancton de 20 µm de mailles ainsi que des mesures de paramètres physico-chimiques ont été faits dans chaque station. L'analyse des données environnementales a montré l'existence d'uneffet intersaison avec des valeurs plus élevées en avril excepté la température. Par ailleurs, un effet d'inter-sites a été observé uniquement en septembre pour la température, la salinité, la conductivité et l'oxygène dissout.En termes de diversité phytoplanctonique, en avril, 49 espèces réparties dans5 classes ont été identifiées dans l'AMP contre 47espèces et 5 classes identifiées à Diomboss et 42 espèces et 5 classes à Sangako. En septembre, 57espèces réparties dans 5 classes ont été répertoriées dans l'AMP contre 54 espèces et 4 classes à Diomboss, et 51 espèces réparties dans 4 classes identifiées à Sangako. Les résultats seuls de la richesse spécifique du phytoplancton ne permettent pas d'apporter une contribution sur l'évaluation de l'efficacité de l'AMP de Bamboung