Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm

Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures

Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis

The complete mitogenome of Fusarium oxysporum f. sp. albedinis (FOA), the causal agent of the destructive fusarium wilt in date palm, is sequenced and assembled. The circular mitogenome of isolate Foa44 is 51,601 bp in length and contains 26 transfer RNA (tRNA) genes, one ribosomal RNA (rRNA), and 28 protein-coding genes. A mitogenome-based phylogenetic analysis of Fusarium revealed that FOA is congruent with previous nuclear-gene phylogenetic results

High-Temperature and Drought Stress Effects on Growth, Yield and Nutritional Quality with Transpiration Response to Vapor Pressure Deficit in Lentil

High temperature and water deficit are among the major limitations reducing lentil (Lens culinaris Medik.) yield in many growing regions. In addition, increasing atmospheric vapor pressure deficit (VPD) due to global warming causes a severe challenge by influencing the water balance of the plants, thus also affecting growth and yield. In the present study, we evaluated 20 lentil genotypes under field conditions and controlled environments with the following objectives: (i) to investigate the impact of temperature stress and combined temperature-drought stress on traits related to phenology, grain yield, nutritional quality, and canopy temperature under field conditions, and (ii) to examine the genotypic variability for limited transpiration (TRlim) trait in response to increased VPD under controlled conditions. The field experiment results revealed that high-temperature stress significantly affected all parameters compared to normal conditions. The protein content ranged from 23.4 to 31.9%, while the range of grain zinc and iron content varied from 33.1 to 64.4 and 62.3 to 99.3 mg kg−1 , respectively, under normal conditions. The grain protein content, zinc and iron decreased significantly by 15, 14 and 15% under high-temperature stress, respectively. However, the impact was more severe under combined temperature-drought stress with a reduction of 53% in protein content, 18% in zinc and 20% in iron. Grain yield declined significantly by 43% in temperature stress and by 49% in the combined temperature-drought stress. The results from the controlled conditions showed a wide variation in TR among studied lentil genotypes. Nine genotypes displayed TRlim at 2.76 to 3.51 kPa, with the genotypes ILL 7833 and ILL 7835 exhibiting the lowest breakpoint. Genotypes with low breakpoints had the ability to conserve water, allowing it to be used at later stages for increased yield. Our results identified promising genotypes including ILL 7835, ILL 7814 and ILL 4605 (Bakria) that could be of great interest in breeding for high yields, protein and micronutrient contents under high-temperature and drought stress. In addition, it was found that the TRlim trait has the potential to select for increased lentil yields under field water-deficit environment

Résilience de la lentille au changement climatique au Maroc : principales réalisations en amélioration génétique, biotechnologie et gestion des cultures

Au Maroc, la lentille est cultivée dans des conditions pluviales et sa productivité est fortement influencée par les aléas climatiques, notamment la quantité et la distribution des précipitations, ainsi que les hautes températures. Dans ce contexte, l’augmentation de la production est tributaire de plusieurs facteurs, notamment l’utilisation de variétés améliorées, la maîtrise de l’itinéraire technique et des bonnes pratiques agricoles permettant une meilleure efficience d’utilisation de l’eau. Les recherches conduites à l’échelle nationale ont abouti au développement des nouvelles variétés améliorées et la mise ne place des nouvelles pratiques culturales, comme le semis direct, qui pourraient aboutir à une meilleure résilience face au changement climatique notamment en termes de tolérance à la sècheresse et aux hautes températures et de mécanisation. En effet, certaines nouvelles variétés sélectionnées lors des expérimentations pluriannuelles ont montré une meilleure tolérance au déficit hydrique et à la chaleur grâce à des caractéristiques morphologiques, phénologiques et physiologiques. D’autre part, des travaux de recherche en caractérisation des ressources génétiques (populations locales, espèces sauvages) ont permis d’identifier des sources de tolérance/résistance à ces stress abiotiques qui ont été intégrées en tant que parents dans la phase amont des programmes de création variétale. Néanmoins, il est important de renforcer les initiatives de transfert de technologies adéquates pour promouvoir l’utilisation des obtentions variétales et des techniques d’adaptation par les agriculteurs afin de mieux valoriser les acquis de recherche. D’autre part, il est essentiel de poursuivre la collection et l’exploration des ressources génétiques et la création des nouvelles variétés en ciblant en priorité les caractères agronomiques, morphologiques, physiologiques et qualitatifs.  Cela répondrait aux besoins des agriculteurs, des consommateurs et des industriels en matière de résilience au changement climatique, de rentabilité et de qualité nutritive. L’intégration des technologies modernes de phénotypage et de génotypage ainsi que l’utilisation des techniques de speed breeding dans le programme d’amélioration génétique est une étape importante pour améliorer le gain génétique et accélérer le développement de nouvelles variétés dotées des traits d’intérêts, notamment la stabilité du rendement face aux variations climatiques caractérisées par les faibles précipitations et la récurrence des épisodes de chaleur

First draft genome assembly of the Argane tree (Argania spinosa)

Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes

First draft genome assembly of the Argane tree (Argania spinosa) [version 2; peer review: 2 approved]

BACKGROUND : The Argane tree (Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. METHODS : Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. RESULTS : In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. CONCLUSION : The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.DATA AVAILABILITY: All of the A. spinosa datasets can be retrieved under BioProject accession number PRJNA294096: http://identifiers.org/ bioproject:PRJNA294096. The raw reads are available at NCBI Sequence Reads Archive under accession number SRP077839: http://identifiers.org/insdc.sra:SRP077839. The complete genome sequence assembly project has been deposited at GenBank under accession number QLOD00000000: http://identifiers. org/ncbigi/GI:1408199612. Data can also be retrieved via the International Argane Genome Consortium (IAGC) website: http://www.arganome.org.https://f1000research.compm2021BiochemistryGeneticsMicrobiology and Plant Patholog

Establishing African genomics and bioinformatics programs through annual regional workshops

The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.</p

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

Isolation and evaluation of the entomopathogenic fungi investigated against the leafhopper Jacobiasca lybica (Hemiptera : Cicadellidae ) under laboratory conditions

editorial reviewedThe control of leafhopper populations is often based on the extensive use chemical insecticides that are known for many side effects on non target organisms, environment, human health and food safety, therefore, the use of entomopathogenic fungi provides a promising biocontrol alternative against the leafhopper. During our study, we investigated, isolated, and evaluated the efficiency of entomopathogenic fungi against Jacobiasca lybica under laborartory conditions. The fungi were isolated from leafhopper collected from a vineyard in the Berkane Province of Morocco, and then they were identified according to micro and marcoscopic aspects before they were tested to evaluate their efficiency against this leafhopper. Our results indicated the presence of many species of fungus that were morphologically different. Four fungi were chosen by their different macroscopic aspects for further identification and pathogenicity tests. The species were identified as C2, C3, C12 and C13 (for intellectual property reason). The pathogenicity test had shown that C3 was the most developed fungus during the five days of the study. This promising result indicated that entomopathogenic fungus selected had shown some effectiveness to develop faster on leafhoppers which can be a possible biological control to use as an integrated management against J. lybica

Chlorophyll content and fluorescence as physiological parameters for monitoring Orobanche foetida Poir. infection in faba bean.

Orobanche spp. are root parasitic plants that cause yield losses in faba bean (Vicia faba L.). In Tunisia, O. crenata and O. foetida are among the major problems limiting faba bean production and productivity. Breeding for resistance and development of resistant varieties remain the most efficient control strategy to combat these parasites. In our study, field trials were conducted over two consecutive cropping seasons. A set of 42 genotypes were used in this study; 39 advanced lines and three checks; Najeh and Baraca (resistant) and Badi (susceptible). The trials were conducted in highly infested O. foetida plot at Oued-Beja Research Station in Tunisia. Results showed that advanced lines XAR-VF00.13-1-2-1-2-1 and XBJ90.04-2-3-1-1-1-2A expressed high resistance level exceeding those recorded for resistance checks Najeh and Baraca. O. foetida significantly affected the biomass, grain yield, chlorophyll content index (CCI) and the maximum quantum efficiency (Fv/Fm ratio). No significant effect was observed on host plant water content (WC). CCI decreases varied from 46.4% for the susceptible check Badi and 4.2% and 9.3%, respectively, for Baraca and XBJ90.04-2-3-1-1-1-2A. Orobanche parasitism resulted in a slight decreases of Fv/Fm ratio for the advanced lines XBJ90.04-2-3-1-1-1-2A and XAR-VF00.13-1-2-1-2-1 against important decreases observed for Badi and Baraca. Correlation between resistance to O. foetida and CCI and Fv/Fm makes this, easy-to-measure, parameter very useful as a practical screening tool for early parasitism detection, diagnosis and identification and selection of high resistant plants against this parasite