To address food and nutrition security in the face of burgeoning global populations and erratic climatic conditions there is a need to include nutrient dense, climatic resilient but neglected indigenous fruit trees in agrifood systems. Here we present the draft genome sequence of Kei Apple, Dovyalis afra, a neglected indigenous African fruit tree with untapped potential to contribute to nutrient security and improved livelihoods. Our long-read-based genome assembly comprises 440 Mbp sequence across 1190 contigs with a N50 and L50 of 13.3 Mbp and 11, respectively. We also annotated the genome and identified 27,449 protein-coding genes. Our genome assembly provides a valuable resource for unlocking the food security and nutraceutical potential of Kei apple.

Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining Nanopore-based assembly with Hi-C scaffolding, we produced a high-quality chromosome-scale assembly with an N50 of 69.5 Mbp. Using transcriptome evidence from Nanopore RNASeq and protein homology evidence from related crops, we predicted and annotated 31,614 putative protein coding genes. We also show how this genome substantially improves anchoring of genetic markers from African yam bean, confirming its significance as a resource for genetic research in African yam bean.

Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis, a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.

One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-representation of researchers in Africa in the genome sequencing efforts of their indigenous orphan crops. Here we report a radically inclusive approach to orphan crop genomics using the case of Lablab purpureus (L.) Sweet (syn. Dolichos lablab , or hyacinth bean) – a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led South-North plant genome collaboration produced a high-quality chromosomescale assembly of the lablab genome – the first chromosome-scale plant genome assembly locally sequenced in Africa. We also re-sequenced cultivated and wild accessions of lablab from Africa confirming two domestication events and examined the genetic diversity in lablab germplasm conserved in Africa. Our approach provides a valuable resource for lablab improvement and also presents a model that could be explored by other researchers sequencing indigenous crops particularly from Low and middle income countries (LMIC).

Purpose: Viral diseases cause severe yield losses and quality decline in crops worldwide. Despite their economic significance, the occurrence and distribution of the major viruses and viroids infecting Taro in Kenya remain poor, limiting the development of robust disease management strategies to mitigate their spread. This study thus aimed to identify the viruses and viroids infecting Taro in Kenya as a basis for developing effective management strategies to support the prevention and control of Taro viruses. Methodology: Viral surveys and sampling were conducted across nine Taro-growing counties with diverse agroecological conditions in Kenya to determine the incidence and distribution of viruses affecting Taro. Leaf and whole plant samples of symptomatic edible and wild Taro were collected for PCR, RT-PCR, and small RNA sequencing assays to determine the diversity of viruses and viroids infecting Taro. Results: Disease-like symptoms, including stunting, leaf rolling, shrinkage, deformed leaves with mosaic and yellow veins, and dwarfism, were observed. An overall mean disease incidence of 32-60% was recorded in all sites surveyed. Small RNA sequencing revealed the presence of both DNA and RNA viruses. Detected DNA viruses included the Taro Bacilliform Virus (TaBV) and Taro Bacilliform CH Virus (TaBCHV), badnaviruses specific to Taro, the sweet potato Badnavirus B, sugarcane bacilliform virus, and sweet potato leaf curl virus. The RNA viruses included the sweet potato feathery mottle and Phaseolus vulgaris alphaendornavirus. A Citrus exocortis viroid was also detected. Interestingly, the wild relatives of Taro displayed very few viral sequence hits. This study reports the Taro viruses and viroids circulating in Kenya and is the first to describe the incidence, distribution, and sequence variability of TaBV in Kenya. Recommendations: Future studies should focus on developing effective management strategies to support the prevention and control of Taro viruses, including genetic resources for virus-Taro interactions, removing infected crops, controlling insect vectors, and developing virus-free planting materials.

Pigeonpea [Cajanus cajan (L.) Millspaugh] is an economically important legume playing a crucial role in the semi-arid tropics. Pigeonpea is susceptible to Helicoverpa armigera (Hübner), which causes devastating yield losses. This pest is developing resistance to many commercially available insecticides. Therefore, crop wild relatives of pigeonpea, are being considered as potential sources of genes to expand the genetic base of cultivated pigeonpea to improve traits such as host plant resistance to pests and pathogens. Quantitative proteomic analysis was conducted using the tandem mass tag platform to identify differentially abundant proteins between IBS 3471 and ICPL 87 tolerant accession and susceptible variety to H. armigera, respectively. Leaf proteome were analysed at the vegetative and flowering/podding growth stages. H. armigera tolerance in IBS 3471 appeared to be related to enhanced defence responses, such as changes in secondary metabolite precursors, antioxidants, and the phenylpropanoid pathway. The development of larvae fed on an artificial diet with IBS 3471 lyophilised leaves showed similar inhibition with those fed on an artificial diet with quercetin concentrations with 32 mg/25 g of artificial diet. DAB staining (3,3′-diaminobenzidine) revealed a rapid accumulation of reactive oxygen species in IBS 3471. We conclude that IBS 3471 is an ideal candidate for improving the genetic base of cultivated pigeonpea, including traits for host plant resistance.

Taro (Colocasia esculenta L. Schott) is an important crop for food and nutrition security, incomes, and livelihood of people in developing countries.Its cultivation and productivity have been limited mainly due to a lack of quality planting materials.Therefore, this study developed an effective micropropagation method for two common taro varieties in Kenya (Purple Wild and Dasheen) using apical meristem derived from portions of the corm and base of leaf petioles.This study optimized the 6benzylaminopurine (BAP) and indole-3-butyric acid (IBA) levels for a better shoot and root development.The highest shoot induction was observed in both varieties when Murashige & Skoog (MS) media was supplemented with 2 mg/L of BAP.Similarly, the maximum rooting response was achieved in both varieties on half-strength MS media supplemented with 0.5 mg/L of IBA.The study also revealed significant interactions between variety × BAP levels and variety × IBA levels (P<0.0001) for shoot and root development, respectively.This apical meristem-based micropropagation method developed in this study can be used for rapid multiplication of genetically clean planting materials for commercial uses and to establish taro transformation protocols.

Insect pests pose a serious threat to global food production. Pod borer (Helicoverpa armigera (Hübner)) is one of the most destructive pests of leguminous crops. The use of host resistance has been an effective, environmentally friendly and sustainable approach for controlling several agricultural pests. The exploitation of natural variations in crop wild relatives could yield pest-resistant crop varieties. In this study, we used a high-throughput transcriptome profiling approach to investigate the defense mechanisms of susceptible cultivated and tolerant wild pigeonpea genotypes against H. armigera infestation. The wild genotype displayed elevated pest-induced gene expression, including the enhanced induction of phytohormone and calcium/calmodulin signaling, transcription factors, plant volatiles and secondary metabolite genes compared to the cultivated control. The biosynthetic and regulatory processes associated with flavonoids, terpenes and glucosinolate secondary metabolites showed higher accumulations in the wild genotype, suggesting the existence of distinct tolerance mechanisms. This study provides insights into the molecular mechanisms underlying insect resistance in the wild pigeonpea genotype. This information highlights the indispensable role of crop wild relatives as a source of crucial genetic resources that could be important in devising strategies for crop improvement with enhanced pest resistance.

We have sequenced the genome of grass pea ( Lathyrus sativus ), a resilient diploid (2n=14) legume closely related to pea ( Pisum sativum ). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

Being sessile, plants must regulate energy balance, potentially via source-sink relations, to compromise growth with survival in stressful conditions. Crops are sensitive, possibly because they allocate their energy resources toward growth and yield rather than stress tolerance. In contrast, resurrection plants tightly regulate sugar metabolism and use a series of physiological adaptations to suppress cell death in their vegetative tissue to regain full metabolic capacity from a desiccated state within 72 h of watering. Previously, we showed that shoots of the resurrection plant Tripogon loliiformis, initiate autophagy upon dehydration as one strategy to reinstate homeostasis and suppress cell death. Here, we describe the relationship between energy status, sugar metabolism, trehalose-mediated activation of autophagy pathways and investigate whether shoots and roots utilize similar desiccation tolerance strategies. We show that despite containing high levels of trehalose, dehydrated Tripogon roots do not display elevated activation of autophagy pathways. Using targeted and non-targeted metabolomics, transmission electron microscopy (TEM) and transcriptomics we show that T. loliiformis engages a strategy similar to the long-term drought responses of sensitive plants and continues to use the roots as a sink even during sustained stress. Dehydrating T. loliiformis roots contained more sucrose and trehalose-6-phosphate compared to shoots at an equivalent water content. The increased resources in the roots provides sufficient energy to cope with stress and thus autophagy is not required. These results were confirmed by the absence of autophagosomes in roots by TEM. Upregulation of sweet genes in both shoots and roots show transcriptional regulation of sucrose translocation from leaves to roots and within roots during dehydration. Differences in the cell's metabolic status caused starkly different cell death responses between shoots and roots. These findings show how shoots and roots utilize different stress response strategies and may provide candidate targets that can be used as tools for the improvement of stress tolerance in crops.

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

Global climate change, increasingly erratic weather and a burgeoning global population are significant threats to the sustainability of future crop production. There is an urgent need for the development of robust measures that enable crops to withstand the uncertainty of climate change whilst still producing maximum yields. Resurrection plants possess the unique ability to withstand desiccation for prolonged periods, can be restored upon watering and represent great potential for the development of stress tolerant crops. Here, we describe the remarkable stress characteristics of Tripogon loliiformis, an uncharacterised resurrection grass and close relative of the economically important cereals, rice, sorghum, and maize. We show that T. loliiformis survives extreme environmental stress by implementing autophagy to prevent Programmed Cell Death. Notably, we identified a novel role for trehalose in the regulation of autophagy in T.loliiformis. Transcriptome, Gas Chromatography Mass Spectrometry, immunoblotting and confocal microscopy analyses directly linked the accumulation of trehalose with the onset of autophagy in dehydrating and desiccated T. loliiformis shoots. These results were supported in vitro with the observation of autophagosomes in trehalose treated T. loliiformis leaves; autophagosomes were not detected in untreated samples. Presumably, once induced, autophagy promotes desiccation tolerance in T.loliiformis, by removal of cellular toxins to suppress programmed cell death and the recycling of nutrients to delay the onset of senescence. These findings illustrate how resurrection plants manipulate sugar metabolism to promote desiccation tolerance and may provide candidate genes that are potentially useful for the development of stress tolerant crops.

Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.

Africa currently faces several opportunities and challenges in terms of genomics research. The continent harbors the richest biodiversity to provide fertile ground for harnessing genomics. On the other hand, it bears the heaviest burden of human diseases (both infectious and chronic) and the effects of climate change, pests, and diseases on native crops and livestock. In spite of the challenges, genomics research and the associated products stand to significantly benefit the region. By adopting genomics research, African researchers can tap into the rich continental diversity, embrace personalized medicine as well as establish crops and livestock breeds with desirable traits. These benefits will not come at an easy cost but the continent has an opportunity to learn from middle-income countries such as Mexico and Brazil that embraced the genomic revolution in a timely fashion. Hence the region should search for homegrown solutions, foster mutually beneficial collaboration, and invest substantially in genomics research.

AFBIX09, First African Virtual Conference on Bioinformatics; BecA, Biosciences Eastern and Central Africa; BMEW, Basic Molecular Evolution Workshop; ILRI, International Livestock Research Institute; RSG EA, Regional Students Group Eastern Africa. Why do we bother to organise scientific meetings? The amount of time, energy and resources they take up always surprises us. They do not help our career and promotion prospects – most hiring committees ignore our involvement in organising and participating in such meetings. So why do we do keep organising them? For us, the reasons why we do continue to organise new meetings are similar to those motivating the funders who support the events: promoting research in areas (topical and geographical) where we feel it is particularly needed; helping promote interactions between researchers; providing high-quality scientific impact, ideally at low cost. Not that we are altruists – we enjoy it too, in particular the opportunity it provides to contribute to the development of the scientific fields we work in. We were recently impressed by the effectiveness with which three events we were involved in achieved these and similar goals (Fig. 1) – we hope that, by sharing our enthusiasm for what was achieved through these meetings, we can encourage others to organise and fund similar projects in the future. An overview of the three events described in the article. To highlight the relationships between the different events, the names of the authors of this article are coloured red. Part of the link between these events was thematic – the topic of molecular evolution playing an important role in all of them. At first glance, this might seem strange for scientists keen to promote development within the African continent – surely there are many more important topics to focus on in that context? However, despite first impressions, molecular evolutionary analyses can contribute to many applications associated with economic and public health issues in Africa. One important set of applications is in the epidemiology of diseases important in Africa. These studies may focus on the evolution of the pathogens themselves, including viruses (such as HIV 1), bacteria (such as Mycobacterium tuberculosis 2) and eukaryotes (such as Plasmodium falciparum 3, one of the causative agents of malaria) – but also the evolution of the vectors responsible for transmitting many important diseases (such as Glossina fuscipes fuscipes 4, tsetse flies that are vectors of sleeping sickness, or Anopheles mosquitoes, important vectors of malaria 5). Other medical applications involve analysis of the molecular basis of disease virulence in pathogens (such as in swine fever virus 6), or disease immunity or resistance in hosts (such as the human Duffy blood group locus, which confers complete resistance to vivax malaria 7). In a very different context, molecular evolutionary analyses have been applied in the fields of conservation and ecological genetics, including analyses of the history and evolution of indigenous species (such as cichlid fishes in the African Great Lakes 8) and prioritisation of endangered species for conservation programs (such as Madagascan lemurs 9). Other applications include attempts to understand the response of organisms to changing climatic conditions 10, crop plant research 11, 12 and analyses of human history and anthropology 13. To tell the story of our work together, we will follow the path taken by Sheila Ommeh, the only one of us involved in all three events. The first of these was the AFBIX09 14, which took place in July 2009. Sheila was an organiser of this event, together with many others including Mtakai Ngara, and Etienne P. de Villiers, co-authors of this current paper. As its name suggests, this was a virtual event, where much of the interaction between participants was mediated by information and communication technologies rather than face-to-face. Crucially, AFBIX09 showed us that virtual technologies can successfully deliver useful, effective scientific interactions, at very low cost. Fourteen scientists were involved in organising and delivering the event; four were keynote speakers, five were invited speakers and five were mentors who supported the various hubs through various funds. It also highlighted key points to be aware of when successfully setting up a virtual event of this kind – several of us summarised these lessons in a recent publication 15. Training can play a key role in promoting development and equality, as recognised by international organisations such as UNESCO and the International Council for Science 16 and the European Union 17. Therefore, increasing the provision and accessibility of training in developing countries could play a key role in bridging the gap between students worldwide. Students in so-called developed countries typically have easier and cheaper access to scientific training courses than their counterparts in developing countries. Part of the reason for this is that most trainers – and therefore most courses – are located in developed countries. With this in mind, several of us wanted to extend our experience of the effectiveness of virtual technologies to the more complicated context of a training course – where two-way interactions between presenter and audience are more diverse and important than for a conference. But how could we find trainers for this virtual course – trainers that could be relied upon to deliver good, relevant training material? This problem was solved by Sheila's attendance of the EMBO Practical Course on Computational Molecular Evolution 18. One of us, Aidan Budd, was an organiser of this course, which took place in May 2010 in Heraklion, Greece, at the Hellenic Centre for Marine Research, Institute of Marine Biology and Genetics. During the ten days of this course, Sheila experienced at first-hand the training of many prominent contributors to the field of molecular evolution, including developers of key software packages such as RAxML 19 (Alexandros Stamatakis), PhyML 20 (Olivier Gascuel), MrBayes 21 (John Huelsenbeck) and PAML 22 (Ziheng Yang). The openness and accessibility of the trainers, coupled with the way the course was organised, made it easy for trainees and trainers to get to know each other – providing great opportunities to develop longer-term relationships. This is exactly what Sheila did; approaching several of the trainers whose presentations covered topics she felt would be particularly useful for African scientists. She invited these trainers to deliver similar material – which she knew was of high educational quality – in a virtual context. Everyone she asked was keen to participate – although unfortunately time constraints meant that not all of those she invited were able to get involved. Using the contacts she made in Heraklion, Sheila, along with many others including co-authors Mtakai Ngara, Isaac Njaci and Etienne P. de Villiers, organised the first ever trans-African virtual bioinformatics training course. The BMEW 23 took place in July 2010, and was organised by the Regional Students Group Eastern Africa (RSG EA) 24 together with Biosciences Eastern and Central Africa (BecA). Financial and logistic support for the course was provided by the International Livestock Research Institute (ILRI) in Nairobi, Kenya. The central hub was located at the ILRI/BecA, accompanied by seven satellite hubs (SMBI Tangier-Morocco, SMBI Casablanca-Morocco, SMBI Rabat-Morocco, SANBI UWC South Africa, UCT South Africa, University of Pretoria and University of Mauritius). The course was attended by 50 trainees – 18 in Kenya, 15 in South Africa, 16 in Morocco and 1 in Mauritius. Four trainers from the Heraklion course made virtual presentations during the course: Maria Anisimova from Zurich, Switzerland; Aidan Budd from Heidelberg, Germany; Carolin Kosiol from Vienna, Austria and Rasmus Nielsen from Copenhagen, Denmark. Several of the trainers included African-specific examples in their presentations, including analyses of vivax malaria resistance in sub-Saharan African populations 7 and cichlids fish diversity in African Great Lakes 8. While presenting, external trainers were able to see and hear a ‘question taker’ who was located at the central Kenyan hub – but were not directly linked in this way to any of the training rooms. This was to avoid overwhelming the trainers with overlapping inputs from multiple different sources – although at the same time this made it harder to carry out two-way interactions between trainer and trainees. However, it was still possible to accept questions from the trainees via the ‘question taker’, and to initiate exercises involving direct interactions between trainees located at the same hub. Cisco's Webex 25, a proprietary, service-oriented software product provided by ILRI's Information and Computational Technology (ICT) department, was used for the online conferencing component of the course. This software can host a maximum of 25 satellite nodes (also referred to as ‘hubs’) situated in different locations and commonly used in scientific webinars e.g. Cambridge Healthtech Institute's Bio-IT World Web Symposia 26. The central hub was located at the ILRI/BecA, with the other seven locations operating as satellite hubs. A Webex server was hosted on a Mac OS X laptop computer, using Ethernet cables for Internet connection, rather than via a wireless network, to obtain better connection stability and enable faster data transfer. Training presentations were transmitted from the central hub to satellite hubs on a 118.675 KBps Internet connection. Remote hubs logged into the Webex system via a range of personal computers (both Windows and Mac OS X), and presentations were broadcasted to the audience using LCD projectors. Trainers delivered their presentations using the Webex clients on their local machines – as the trainer moved to a new slide, that new slide was shown almost instantly to the other hubs. Prior to the course, tests were carried out with coordinators of the satellite hubs, and with the trainers, to identify potential problems and accustom them to the technology. During the course, trainee questions were communicated to trainers via the central hub, using voice connection and the chatting capabilities of Skype software 27. opportunities to network with participants in different locations, very cost-effective training provision, direct access provided to scientific experts in the field, no fee or travel/accommodation expenses for participants (both trainees and trainers). All trainees indicated that they would like to see such virtual courses held on a regular basis, in particular with focus on topics of specific relevance to the continent. At the same time, participants suggested several ways in which the educational experience could have been improved – and in which more trainees could have been attracted to attend. It was felt that trainees would have attended if the course had been held while the participating universities were in session, rather than during the holidays. The stability of the Internet connection at some of the satellite hubs was also an issue, preventing several hubs from participating. Others felt that more trainees would have attended if the advertisement period for the course had been longer, making it easier for people to plan their attendance. Most trainees would have liked access to recordings of the sessions to be available after the virtual workshop was over. The key feedback received from the trainers was that they would have liked more opportunity for two-way interaction between trainer and audience. They acknowledged, however, that it could be difficult to achieve this without overloading the trainer with input from multiple sources. Overall, however, the trainers were impressed with the enthusiasm and commitment of the organisers – especially the prompt, enthusiastic, friendly, and efficient response to logistic and software issues. Finally, the trainers were pleased to learn through their own experience that this kind of teaching can be effective. In particular, Aidan Budd is involved with a group of European bioinformatics trainers, the Bioinformatics Training Network 28, aiming to improve and coordinate bioinformatics training in Europe. Several members of the BTN want to develop the use of virtual technologies to increase the impact of current training activities 29. As a result of his involvement in the BMEW, Aidan now has much more confidence in the effectiveness of virtualised courses, and is keen to develop these ideas further, and become involved in further virtual projects. In the light of this feedback, and of our own experiences organising the course, we hope to organise more virtual courses in the future. Virtual courses hold great potential for Africa and so-called developing countries in general as an efficient and cost-effective way of improving and increasing training provision. Expanding the program of virtual courses on offer will need a community of high-calibre trainers willing to participate in the courses – the limited and unusual interaction between trainers and trainees in virtual courses makes it particularly important that the trainers are both experienced and flexible in their presentation style. Other ways of increasing the impact of virtual courses are to increase both the number of hubs involved in the events, and the number of participants attending at each hub – which will be helped by the newly installed Africa-traversing fibre optic cable network. However, it is also clear that expansion of this kind will require increased support from funding bodies for virtual activities. Hopefully, the successful interplay between virtual and regular events we have described here will encourage organisations to provide additional funding and support for activities of this kind. Finally, we find it interesting to note that a key part of the development of the virtual course was a regular, non-virtual course. The regular course provided the social and scientific environment needed to establish and develop good, long-term relationships within the community relationships that led to the acquisition of good, committed and reliable trainers for the virtual course. The authors wish to acknowledge the contributions of Allan Orth, Sonal Patel, Nelson Gichora, Kimita Gathii, Geoffrey Mtenyo, scientific mentors, and all the hub coordinators for making the BMEW a success. They also want to thank their fellow organisers, and the funders, of both AFBIX09 and the EMBO Practical Course on Computational Molecular Evolution. Aidan Budd would like to thank Toby Gibson for supporting his participation in the BMEW and the EMBO Practical Course on Computational Molecular Evolution, Vera Herkommer for her advice and help concerning documents and publications produced by international organisations, and Maria Pia Becker for many useful suggestions and comments on an earlier version of the text.

Research in this thesis focussed on the improvement of agricultural crops in increasing water use efficiency that impacts global crop productivity. The study identified key genetic regulatory mechanisms that the resurrection plant Tripogon loliiformis utilises to tolerate desiccation. Due to the conserved nature of the pathways involved, this information can be transferred for the enhancement of drought tolerance and water use efficiency in agricultural crops. Specifically this study used high throughput sequencing, microscopy and plant transformation to further the understanding of post-transcriptional regulatory mechanisms. It was shown that T. loliiformis uses microRNAs to regulate pro-survival autophagy pathways to tolerate desiccation.