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Although Bathycoccus is one of the most abundant picophytoplankton, little is known about the genetic diversity underlying its adaptation to ecological niches. In this study, the diversity of Bathycoccus populations during their annual bloom in the Mediterranean bay of Banyuls France was assessed by an INDEL based approach. Oxford Nanopore Technology (ONT) was used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in Banyuls. Data in this repository correspond to the raw sequencing data and the genome assemblies produced from 7 strains of Bathycoccus prasinos from the Roscoff Culture Collection (RCC : https://roscoff-culture-collection.org/). For whole genome sequencing by Oxford Nanopore technology (ONT), DNA was extracted by a CTAB method from 100 ml culture. ONT libraries were barcoded using the Rapid Barcoding Sequencing (SQK-RBK004) and deposited on R9.4 flow cell. Raw ONT Fast5 data were basecalled using Guppy 4.0.5 and the HAC model, and QC performed using NanoPlot 1.38.1. All reads with a QPHRED higher than 8 were retained and subject to genome assembly using Flye 2.8 under standard options. Raw assemblies were then polished with 3 turns of standard Racon after mapping of raw reads on the previous sequence using minimap2 (-ax map-ont mode). Final scaffolding was performed using Ragoo 1.1 upon the original B. prasinos reference genome (GCA_002220235.1). Final QC of assemblies was performed using QUAST 5.0.

We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar.FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference.FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis.We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.

International audience; Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1 . HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles.

Le palmier rônier ou Borassus aethiopum Mart. est une plante aux multiples usages, qui présente des caractéristiques socio-économiques importantes pour les populations locales. Les nombreux avantages dont offre la plante, font qu'elle subit de grandes pressions anthropiques. Dans le but de définir des stratégies de gestion et de conservation à moyen et long terme, une analyse de la diversité a été effectuée grâce aux marqueurs microsatellites spécifiques de l'espèce. Ces derniers ont été développés à partir d'un séquençage partiel du génome de B. aethiopum, puis par la méthode QDD, onze (11) amorces spécifiques ont pu être définies et testées sur 180 échantillons représentant neuf (9) populations au Bénin. L'utilisation de ces marqueurs a permis de distinguer deux groupes génétiques dont l'un est constitué des populations Sud et Centre Bénin et le second groupe représentant l'ensemble des populations du Nord y compris la population de Savè qui est aussi située au Centre Bénin. De plus, dans le souci d'élucider la frontière génétique entre les différentes espèces de Borassus sp., les analyses phylogénétiques conduites sur l'ensemble des échantillons issus des cinq espèces (B. aethiopum, B. akeassii, B. madagascariensis, B. heineaus, B. flabellifer) ont permis de déterminer que l'espèce soeur de B. aethiopum serait B. madagascariensis avec une spéciation intervenue il y a trois (03) millions d'années (Ma). Ces résultats sont d'une grande importance et amélioreront l'état des connaissances aussi bien sur B. aethiopum que les autres espèces. Tout ceci contribuera à une meilleure gestion de l'espèce dans son aire de distribution.

The African fan palm Borassus aethiopum Mart. is widely distributed in savanna ecosystems throughout of the continent. It is an important non-timber forest product with multiple usages of significant socio-economic importance for local populations. As such, it is under strong anthropogenic pressures that have the potential to affect negatively the genetic diversity of the species. However, in spite of its role for fighting both desertification and poverty, the African fan palm remains under-studied, which hampers its sustainable development as a resource. In the present study, we analyze the genetic diversity and population structure of B. aethiopum sampled in different locations across Benin, West Africa. In order to achieve this, we have generated a partial, low-cover genomic sequencing of this species, using a high-throughput sequencing technology, and used it to identify microsatellite loci in the fan palm genome. Among these potential target loci, 11 were found to yield polymorphic amplifications between our test samples and were subsequently used in our analyses. Our results highlight the overall low genetic diversity of Borassus aethiopum populations in Benin, with number of effective alleles ranging from one point forty-four to two point zero sixty-nine per locus, and expected heterozygosity (He) ranging from zero point two hundred and sisty-three to zero point four hundred and fifty-one depending on the population. Moreover, our Bayesian analysis shows that Beninese fan palm populations are mostly structured according to geographic distances, with two population cluster including samples from the Southern and Central geo-climatic regions vs. samples from the Northern region, respectively. The present work constitutes a first step towards larger-scale genetic studies dedicated to B. aethiopum and, beyond that, provides new molecular data to the palm community.

Additional file 2. List of sampled Borassus aethiopum individuals. M, F: male or female palm, respectively. All geographic coordinates are provided as North from the Equator (latitude) and East from the Greenwich meridian (longitude), respectively.

Additional file 4. Results of the Bayesian cluster analysis with variable values of K. Graphical summary generated from STRUCTURE results by CLUMPAK’s main pipeline with values of K ranging from 1 to 10.

Cultivated diversity is considered an insurance against major climatic variability. However, since the 1980s, several studies have shown that climate variability and agricultural changes may already have locally eroded crop genetic diversity. We studied pearl millet diversity in Senegal through a comparison of pearl millet landraces collected 40 years apart. We found that more than 20% of villages visited in 1976 had stopped growing pearl millet. Despite this, its overall genetic diversity has been maintained but differentiation between early- and late-flowering accessions has been reduced. We also found stronger crop-to-wild gene flow than wild-to-crop gene flow and that wild-to-crop gene flow was weaker in 2016 than in 1976. In conclusion, our results highlight genetic homogenization in Senegal. This homogenization within cultivated pearl millet and between wild and cultivated forms is a key factor in genetic erosion and it is often overlooked. Improved assessment and conservation strategies are needed to promote and conserve both wild and cultivated pearl millet diversity.

Microsatellites were designed and characterized in the African fruit tree species Dacryodes edulis (Burseraceae). The fruits are commercialized throughout Central Africa and the species is present in forested environments as well as cultivated systems. The high variability of these markers makes them suitable to investigate the structure of genetic diversity in this important food tree species from Central Africa. From a genomic library obtained by next-generation sequencing, 21 new polymorphic microsatellite loci were developed. Tested on 95 individuals from four populations coming from three countries of the Congo Basin, the microsatellites displayed two to 20 alleles (mean 7.5; expected heterozygosity 0.003 to 0.937, mean 0.666). The transferability of microsatellites was effective for four other Dacryodes species (D. buettneri, D. igaganga, D. osika, D. pubescens). This set of newly developed microsatellite markers will be useful for assessing the genetic diversity and differentiation as well as gene flow patterns of D. edulis in tropical forests from Central Africa.

Yam, a tuber crop, was domesticated alongside some African cereals and defines a cradle of domestication in West Africa., While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

International audience; Premise Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. Methods and Results The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. Conclusions Our protocol could also be generalized to capture long sequences from specific nuclear fragments.

Aim Palaeoecological records indicate that Pleistocene glaciations affected the African rain forest, probably causing its fragmentation, which could explain phylogeographical breaks documented in many tree species. This refuge hypothesis was further tested through species distribution models, hindcasting persistence during the Last Glacial Maximum. However, previous studies failed to estimate with sufficient precision the divergence time between phylogeographical entities to confirm their Pleistocene origin. Developing genomic tools on a representative tree of mature rain forests, we test if parapatric genetic clusters documented in widespread tree species can be interpreted as the legacy of past population fragmentation during the last glacial period(s). Location Tropical Africa, Guineo-Congolian forests. Taxon Greenwayodendron (Annonaceae). Methods To further test the Pleistocene refuge hypothesis by molecular dating, we sequenced the plastome of 145 individuals of the shade-tolerant rain forest tree Greenwayodendron suaveolens and congeneric species, and genotyped the same samples using nuclear microsatellites to identify genetic clusters. Results Five plastid phylogroups of G. suaveolens occur in parapatry throughout Central Africa, following a spatial pattern generally congruent with genetic clusters. Four of them diverged 3.5-4.5 Ma, whereas the fifth one, located in the Cameroon volcanic line (CVL), diverged 8.3 Ma, in the range of divergence times between Greenwayodendron species, highlighting the key role of the CVL in hosting ancient lineages. Within phylogroups, most nodes were dated from 0.9 to 3.2 Myr and a correlation between haplotype divergence and spatial distance was still perceptible, indicating a slow population dynamic. Main conclusions The phylogeographical structures of Central African trees probably established during the Pliocene or early Pleistocene, and while they might have been reinforced during subsequent glacial-interglacial cycles, interglacial phases did not lead to genetic homogenization. Therefore, interpreting phylogeographical patterns of African trees must account for a much deeper past than previously assumed, and cannot be limited to the last glacial period.

Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019; Testar se e como populações naturais são adaptadas ao seu ambiente local e prever suas respostas em função das alterações futuras do habitat é de importância fundamental diante do cenário de mudanças climáticas. Este é o caso dos cafeeiros, em que o ritmo das alterações climáticas pode ser rápido e drástico para a adaptação das populações. Usando a distribuição geográfica de populações selvagens com habitats contrastantes, o objetivo do presente estudo foi identificar polimorfismos de nucleotídeo único (SNPs) em genes candidatos (GCs) identificados como estando envolvidos na adaptação de populações de Coffea canephora da Uganda ao seu ambiente local. Em particular, modificações que ocorrem próximos e/ou em genes relacionados à tolerância aos estresses abióticos tornam esses GCs alvos, potenciais determinantes adaptativos das plantas em função das mudanças climáticas. Ao identificar os fatores ambientais que impulsionam esses processos, torna-se possível prever a adaptabilidade esperada das populações para o clima local futuro.

Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019; A captura direcionada de sequências acoplada ao sequenciamento de alto rendimento tornou-se um método poderoso para o estudo da variação de sequências genômicas. Usando o genoma disponível de C. canephora (tamanho estimado de 710 Mb/haplóide) como referência, projetamos sondas para 323 genes candidatos selecionados (CGs) visando capturar seus homeólogos em 293 acessos de C. canephorada Uganda, 12 clones do Brasil e um subconjunto de 19 indivíduos cobrindo todos os grupos de diversidade de C. canephora. Para um total de 324 indivíduos de C. canephora, projetamos, com sucesso, cerca de 19.000 sondas e identificamos mais de 16.000 polimorfismos de nucleotídeo único (SNPs) de qualidade, localizados dentro ou próximo a 318 genes anotados, gerando dados genotípicos para populações que estão localizadas em regiões que abrangem diferentes condições climáticas. Nós investigamos questões como desenho das sondas, cobertura do sequenciamento, eficiência da hibridização e captura,e estratégias de análise dos dados por bioinformática.