Genetic diversity and race composition of sunflower broomrape populations from Tunisia

Sunflower broomrape (Orobanche cumana Wallr.) was detected in 2010 for the first time in sunflower fields of Tunisia, in the Béja region. No information is available on the race composition and genetic diversity of the broomrape populations parasitizing sunflower in that area. Plant tissue and seeds were collected from nine populations in Béja Sud (ORD, ORE), Amdoun (ORF, ORG), and Béja Nord (ORH to ORL) areas of the Béja region. Virulence studies on populations ORD, ORH and ORK revealed that the ORD population was essentially race E, whereas race G individuals were present in ORH and ORK poulations, with greater frequency in the ORK population. Cluster analysis of inter-population relatedness indicated that Tunisian populations were more related to Eastern European than to Spanish populations, with the Béja Nord populations clustering separately from the rest of Tunisian populations. Analysis at the intra-population level of the ORD, ORG, ORH and ORK populations revealed the existence of two gene pools (GP1 and GP2), that were present in all populations at different frequencies. GP2 was at a lower frequency (1/14) in ORD and ORG but at higher frequencies in ORH (5/15) and ORK (8/14). This indicates that GP1 was probably an initial introduction of a race E population, while GP2 is most likely a later introduction of a race G population, introduced initially in Béja Nord area but now spreading to other areas in the region. The risk of a generalized expansion of race G of broomrape in this sunflower cultivation area is discussed

Molekularna tipizacija tuniskih klonova vrste Myzus persicae (Hemiptera: Aphididae) pomoću mikrosatelitskih biljega

In order to assess the genetic differentiation among Tunisian clones belonging to the Myzus persicae complex (M. persicae (Sulzer), M. antirrhinii (Macchiati) and M. nicotianea Blackman), the molecular technique of microsatellites was used in this study. These markers offer sensitivity and are useful in population genetic studies of parthenogenetic organisms. Here, nine polymorphic microsatellite loci were amplified to distinguish between six parthenogenetic clones belonging to M. persicae complex collected from two different Tunisian areas. Interestingly, this technique allowed discrimination between five different genotypic classes among the six clones. Furthermore, analysis of genetic relatedness between the genotypic classes revealed that two Tunisian clones did not cluster either in M. persicae or in M. antirrhinii taxa, whereas, the four other Tunisian clones clustered into the M. persicae Sulzer taxa.U cilju utvrđivanja genetičkih razlika između tuniskih klonova kompleksa Myzus persicae (Sulzer), M. antirrhinii (Macchiati) i M. nicotianea (Blackman) upotrijebljena je molekularna mikrosatelitska tehnika. Ovi su biljezi vrlo osjetljivi i korisni u takvim istraživanjima partenogenetskih organizama. Umnoženo je devet polimorfnih lokusa mikrosatelita kako bi se razlikovalo šest partenogenetskih klonova kompleksa M. persicae sabranih u dva različita područja u Tunisu. Zanimljivo je da je ova tehnika omogućila razlikovanje između pet različitih genotipskih razreda tih šest klonova. Nadalje, analize genetičke srodnosti između genotipskih razreda pokazale su da dva tuniska klona nisu u istoj grupi niti s M. persicae, niti s M. antirrhinii, dok se četiri tuniska klona nalaze unutar vrste M. persicae Sulzer

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

Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato

[EN] Tomato spotted wilt virus (TSWV) causes severe losses of tomato crops worldwide. To cope dynamically with such a threat, plants deploy strategies acting at the molecular and the epigenetic levels. We found that tomato symptoms progress in a specific-genotype-manner upon TSWV infection. Susceptible genotypes showed within the Auxin Response Factor (ARF8) promoter coupled to enhanced expression of miRNA167a, reduced ARF8 gene and decreased levels of the hormone auxin. This constitutes a deliberate attempt of TSWV to disrupt plant growth to promote spread in sensitive cultivars. Epigenetic regulation through the level of cytosine methylation and the miR167a-ARF8 module are part of a complex network modulating auxin-triggered synthesis and shaping tomato responses to TSWV. Furthermore, modulation of miR167a-ARF8 regulatory module could be applied in tomato-resistance breeding programsThis work was financially supported by the Ministry of Higher Education and Scientific Research of TunisiaWerghi, S.; Aparicio Herrero, F.; Fakhfakh, H.; Gorsane, F. (2021). Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato. Gene. 804:1-10. https://doi.org/10.1016/j.gene.2021.145905S11080

Molecular detection and characterization of <i>Hop stunt viroid</i> sequence variants from naturally infected pomegranate (<i>Punica granatum </i>L.) in Tunisia

Tunisian pomegranate Hop stunt viroid (HSVd) variants are described. Dot-blot hybridization, S-Page, and reverse transcription polymerase chain reaction (RT-PCR) of RNA extracts from infected tissues were carried out. Results obtained by these techniques were confirmed by cDNA sequencing. The genetic diversity among the Tunisian variants was investigated, which also involved analysis of sequences of previously described HSVd variants from Tunisian citrus var. clementine and fig, and from fruit trees from other Mediterranean countries. Phylogenetic analysis showed that Tunisian pomegranate HSVd variants were clustered into two groups: a cachexia strain within the citrus type group and a recombinant citrus-plum type group. Results also showed a high haplotype diversity which was not related either to the host or to the geographical origin. Selective neutrality and genetic network tests suggest that the HSVd isolates have spread rapidly

Molecular detection and characterization of Hop stunt viroid sequence variants from naturally infected pomegranate (Punica granatum L.) in Tunisia

Tunisian pomegranate Hop stunt viroid (HSVd) variants are described. Dot-blot hybridization, S-Page, and reverse transcription polymerase chain reaction (RT-PCR) of RNA extracts from infected tissues were carried out. Results obtained by these techniques were confirmed by cDNA sequencing. The genetic diversity among the Tunisian variants was investigated, which also involved analysis of sequences of previously described HSVd variants from Tunisian citrus var. clementine and fig, and from fruit trees from other Mediterranean countries. Phylogenetic analysis showed that Tunisian pomegranate HSVd variants were clustered into two groups: a cachexia strain within the citrus type group and a recombinant citrus-plum type group. Results also showed a high haplotype diversity which was not related either to the host or to the geographical origin. Selective neutrality and genetic network tests suggest that the HSVd isolates have spread rapidly

Incidence of potato viruses and characterisation of Potato virus Y variability in late season planted potato crops in Northern Tunisia

International audienceSurveys were conducted of symptomatic potato plants in late season crops, from the major potato production regions in Northern Tunisia, for infection with six common potato viruses. The presence of Potato leafroll virus (PLRV), Potato virus Y (PVY), Potato virus X (PVX), Potato virus A (PVA), Potato virus S (PVS) and Potato virus M (PVM) was confirmed serologically with virus infection levels up to 5.4, 90.2, 4.3, 3.8, 7.1 and 4.8%, respectively. As PVY was prevalent in all seven surveyed regions, further biological, serological and molecular typing of 32 PVY isolates was undertaken. Only one isolate was shown to induce PVYO-type symptoms following transmission to tobacco and to react only against anti-PVYO-C antibodies. Typical vein necrosis symptoms were obtained from 31 samples, six of which reacted against both anti-PVYN and anti-PVYO-C antibodies showing they contained mixed isolates, while 25 of them reacted only with anti-PVYN antibodies. An immunocapture RT-PCR molecular test using a PVYNTN specific primer pair set in the 5’NTR/P1 genomic region and examination of recombinant points in three genomic regions (HC-Pro/P3, CI/NIa and CP/3’NTR) showed that all 25 serotype-N PVY isolates were PVYNTN variants with similar recombinations to the standard PVYNTN-H isolate. This is the first report of the occurrence of the PVYNTN variant and its high incidence in late season potatoes in Tunisia

A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest