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The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.

The African livestock sector plays a key role in improving the livelihoods of people through the supply of food, improved nutrition and consequently health. However, its impact on the economy of the people and contribution to national GDP is highly variable and generally below its potential. This study was conducted to assess the current state of livestock phenomics and genetic evaluation methods being used across the continent, the main challenges, and to demonstrate the effects of various genetic models on the accuracy and rate of genetic gain that could be achieved. An online survey of livestock experts, academics, scientists, national focal points for animal genetic resources, policymakers, extension agents and animal breeding industry was conducted in 38 African countries. The results revealed 1) limited national livestock identification and data recording systems, 2) limited data on livestock production and health traits and genomic information, 3) mass selection was the common method used for genetic improvement with very limited application of genetic and genomic-based selection and evaluation, 4) limited human capacity, infrastructure, and funding for livestock genetic improvement programmes, as well as enabling animal breeding policies. A joint genetic evaluation of Holstein-Friesian using pooled data from Kenya and South Africa was piloted. The pilot analysis yielded higher accuracy of prediction of breeding values, pointing to possibility of higher genetic gains that could be achieved and demonstrating the potential power of multi-country evaluations: Kenya benefited on the 305-days milk yield and the age at first calving and South Africa on the age at first calving and the first calving interval. The findings from this study will help in developing harmonized protocols for animal identification, livestock data recording, and genetic evaluations (both national and across-countries) as well as in designing subsequent capacity building and training programmes for animal breeders and livestock farmers in Africa. National governments need to put in place enabling policies, the necessary infrastructure and funding for national and across country collaborations for a joint genetic evaluation which will revolutionize the livestock genetic improvement in Africa.

Africa, a continent of 1.3 billion people, had 326 researchers per one million people in 2018 (Schneegans, 2021; UNESCO, 2022), despite the global average for the number of researchers per million people being 1368 (Schneegans, 2021; UNESCO, 2022). Nevertheless, a strong research community is a requirement to advance scientific knowledge and innovation and drive economic growth (Agnew, et al., 2020; Sianes, et al., 2022). This low number of researchers extends to scientific research across Africa and finds resonance with genomic projects such as the African BioGenome Project (Ebenezer, et al., 2022).The African BioGenome project (AfricaBP) plans to sequence 100,000 endemic African species in 10 years (Ebenezer, et al., 2022) with an estimated 203,000 gigabases of DNA sequence. AfricaBP aims to generate these genomes on-the-ground in Africa. However, for AfricaBP to achieve its goals of on-the-ground sequencing and data analysis, there is a need to empower African scientists and institutions to obtain the required skill sets, capacity and infrastructure to generate, analyse, and utilise these sequenced genomes in-country.The Open Institute is the genomics and bioinformatics knowledge exchange programme for the AfricaBP (Figures 1 & 2). It consists of 10 participating institutions including the University of South Africa in South Africa and National Institute of Agricultural Research in Morocco. It aims to: develop biodiversity genomics and bioinformatics curricula targeted at African scientists, promote and develop genomics and bioinformatics tools that will address critical needs relevant to the African terrain such as limited internet access, and advance grassroot knowledge exchange through outreach and public engagement such as quarterly training and workshops.

The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community (https://bovinepangenome.github.io/). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection., Genome Biology, 24 (1), ISSN:1474-760X

Animal production in low- and middle-income countries (LMICs), predominantly smallholder systems, faces considerable challenges. Low productivity, exposure to multiple pathogens, and climate-related stresses all cause major animal health and welfare issues. Unless addressed, these challenges will continue to negate initiatives aiming for sustainable animal production. To address this, the Royal (Dick) School of Veterinary Studies jointly established the Centre for Tropical Livestock Genetics and Health (CTLGH) with partners in Nairobi and Edinburgh (https://www.ctlgh.org/) to apply genetic improvement for improved animal productivity, health, and welfare in LMICs.

Chickens are an important resource for smallholder farmers who raise locally adapted, genetically distinct breeds for eggs and meat. The development of efficient reproductive technologies to conserve and regenerate chicken breeds safeguards existing biodiversity and secures poultry genetic resources for climate resilience, biosecurity, and future food production. The majority of the over 1600 breeds of chicken are raised in low and lower to middle income countries (LMICs) under resource limited, small scale production systems, which necessitates a low tech, cost effective means of conserving diversity is needed. Here, we validate a simple biobanking technique using cryopreserved embryonic chicken gonads. The gonads are quickly isolated, visually sexed, pooled by sex, and cryopreserved. Subsequently, the stored material is thawed and dissociated before injection into sterile host chicken embryos. By using pooled GFP and RFP-labelled donor gonadal cells and Sire Dam Surrogate (SDS) mating, we demonstrate that chicks deriving entirely from male and female donor germ cells are hatched. This technology will enable ongoing efforts to conserve chicken genetic diversity for both commercial and small holder farmers, and to preserve existing genetic resources at poultry research facilities.

Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group of 38 participants. The final list of 20 issues includes topics spanning from the political (the regulation of genomic data, increased philanthropic funding and malicious uses of neurochemicals) to the environmental (crops for changing climates and agricultural gene drives). The early identification of such issues is relevant to researchers, policy-makers and the wider public.

The cattle tick Rhipicephalus microplus is the most important arthropod vector of livestock diseases globally. Since its introduction in West Africa a decade ago, it has been reported in Ivory Coast, Benin, Togo, Mali, Burkina Faso and Nigeria with potentially far-reaching adverse impacts on the livestock sector in the region. Cameroon is located on a major route for transboundary cattle trade between Central and West Africa and it is therefore at risk from R. microplus invasion. This study investigated the occurrence of R. microplus in Cameroon, the genetic polymorphism of the tick and population structure of isolates from different regions of the country to provide data that underpin the design of future vector control programs.A cross-sectional survey was conducted in which ticks were collected from cattle at 54 sites across the five Agroecological zones (AEZs) within Cameroon. Tick identity (sex and species) was assigned using taxonomic keys. Species identity was confirmed through amplification and sequencing of the mitochondrial COI and 16S rRNA genes. A total of 7091 ticks were collected out of which 1112 (15.6%) were morphologically identified as R. microplus. The presence of R. microplus was confirmed in 4 out of 5 agroecological zones. Only two haplotypes were identified by both COI and 16S rRNA genes, indicating a very low divergence in the genetic structure of the R. microplus population in Cameroon. 16S rRNA sequence analysis revealed a new haplotype specific to Cameroon. Phylogenetic trees revealed that all isolates of R. microplus from Cameroon were grouped into the previously described Africa/Americas clade. Application of a niche modelling algorithm to R. microplus distribution in Cameroon predicted that suitable habitat for the tick extended into southern Nigeria.This study demonstrated for the first time the presence of R. microplus in Cameroon. Genetic diversity tests indicate that the tick has not evolved significantly since the initial introduction to West Africa. We suggest further longitudinal studies to better define the spatial and temporal expansion of the range of the tick and the drivers of this spread.

Additional file 9: Table S7. Distribution of Tp1 gene alleles of T. parva from cattle and buffalo in the sub-Saharan region of Africa.

Additional file 1: Table S1. Cattle blood sample distribution across agro-ecological zones.

Additional file 6: Table S5. Tp1 and Tp2 genes alleles with their corresponding antigen variants.

Additional file 4: Figure S3. Rhipicephalus annulatus dorsal and ventral views.

Additional file 7: Figure S6. Rhipicephalus decoloratus dorsal and ventral views.

Additional file 10: Figure S9. Rhipicephalus microplus dorsal and ventral views.

Additional file 12: Figure S4. Phylogenetic tree showing the relationships among concatenated Tp1 and Tp2 nucleotide sequences of 93 T. parva samples from cattle in DRC and Burundi.

Additional file 3: Table S3. Characteristics of 119 T. parva samples obtained from cattle in different agro-ecological zones (AEZs) of The Democratic Republic of Congo and Burundi.

Additional file 5: Table S4. Estimates of evolutionary divergence between gene alleles for Tp1 and Tp2, using proportion nucleotide distance.

Additional file 3: Figure S2. Hyalomma truncatum and Hyalomma rufipes dorsal and ventral views.

Additional file 2: Table S2. Nucleotide and amino acid sequences of Tp1 and Tp2 antigen epitopes from T. parva Muguga reference sequence.

Additional file 10: Table S8. Distribution of Tp2 gene alleles of T. parva from cattle and buffalo in the sub-Saharan region of Africa.

Background The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa. Methods Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution. Results Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa. Conclusions Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes. Electronic supplementary material The online version of this article (10.1186/s13071-018-2904-7) contains supplementary material, which is available to authorized users.

Theileria parva is a protozoan parasite transmitted by the brown ear tick Rhipicephalus appendiculatus that causes East Coast fever (ECF) in cattle, resulting in substantial economic losses in the regions of southern, eastern and central Africa. The schizont form of the parasite transforms the bovine host lymphocytes into actively proliferating cancer-like cells. However, how T. parva causes bovine host cells to proliferate and maintain a cancerous phenotype following infection is still poorly understood. On the other hand, current efforts to develop improved vaccines have identified only a few candidate antigens. In the present paper, we report the first comparative transcriptomic analysis throughout the course of T. parva infection. We observed that the development of sporoblast into sporozoite and then the establishment in the host cells as schizont is accompanied by a drastic increase of upregulated genes in the schizont stage of the parasite. In contrast, the ten highest gene expression values occurred in the arthropod vector stages. A comparative analysis showed that 2845 genes were upregulated in both sporozoite and schizont stages compared to the sporoblast. In addition, 647 were upregulated only in the sporozoite whereas 310 were only upregulated in the schizont. We detected low p67 expression in the schizont stage, an unexpected finding considering that p67 has been reported as a sporozoite stage-specific gene. In contrast, we found that transcription of p67 was 20 times higher in the sporoblast than in the sporozoite. Using the expression profiles of recently identified candidate vaccine antigens as a benchmark for selection for novel potential vaccine candidates, we identified three genes with expression similar to p67 and several other genes similar to Tp1 - Tp10 schizont vaccine antigens. We propose that the antigenicity or chemotherapeutic potential of this panel of new candidate antigens be further investigated. Structural comparisons of the transcripts generated here with the existing gene models for the respective loci revealed indels. Our findings can be used to improve the structural annotation of the T. parva genome, and the identification of alternatively spliced transcripts.

Table S2. cox1 and 12S rRNA BLAST results for species identification and confirmation. (DOCX 16 kb)

Table S6. Rhipicephalus appendiculatus 12S rRNA haplotypes and their distribution among agro-ecological zones of the Great lakes region and other sub-Saharan African countries. (DOCX 15 kb)

Figure S2. Neighbor-joining tree of 12S haplotype sequences for R. appendiculatus across African countries. (DOCX 18 kb)

Table S4. Population genetic structure inferred by analysis of molecular variance (AMOVA) based on cox1 sequences of R. appendiculatus from different agro-ecological zones. (DOCX 13 kb)

Figure S2. Size and frequency of de novo-assembled representative contigs with high similarity to known viruses. In total 68 samples were sequenced and analyzed. Contig size is represented in 0.5 Kb increments in the X axis. The Y axis represents the number of contigs per size class. For each virus, the number of samples categorized as infected is indicated. a MCMV. b SCMV. c MSV. d MYDV-RMV. (PDF 278Â kb)

Figure S1. cox1 mismatch distribution pattern for R. appendiculatus haplogroup A in different agro-ecological zones. (DOCX 193 kb)

Table S3. Polymorphism in the 22 haplotypes of the cox1 gene fragment of R. appendiculatus. (DOCX 21 kb)

Table S1. Rhipicephalus appendiculatus cox1 and 12S rRNA haplotype sequences retrieved from GenBank. (DOCX 16 kb)

Table S5. Evolutionary neutrality, demographic and spatial history of mitochondrial cox1 gene. (DOCX 15 kb)

Figure S3. Partial nucleotide sequence alignment of Kenya samples in group 1, 2 and 3 relative to the Ohio isolate of SCMV (JX188385.1). The coat protein detected in the original description of maize lethal necrosis in Kenya was used for comparison (JX286708.1) [6]. Alignment was generate using MAFFT. NIb and coat protein coding sequences are color coded blue and red, respectively. Coordinates are based on the Ohio isolate (JX188385.1). In group 1 no nucleotide insertions or deletions were observed. Nucleotide substitutions resulted in amino acid substitutions. Group two, had a 39Â nt deletion (8487 to 8525) that resulted in an in-frame deletion of 13 amino acids. Group 3, had low similarity and a 45Â nt deletion between nt 8487 to 8676 that resulted in a 15-amino acid deletion. (PDF 256Â kb)

RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PDF 84 kb)

Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like virus. (PDF 1.5 MB)

A culture-independent approach was used to elucidate the microbial diversity and structure in the anaerobic-aerobic reactors integrated with a constructed wetland for the treatment of tannery wastewater in Modjo town, Ethiopia. The system has been running with removal efficiencies ranging from 94%-96% for COD, 91%-100% for SO4(2-) and S(2-), 92%-94% for BOD, 56%-82% for total Nitrogen and 2%-90% for NH3-N. 16S rRNA gene clone libraries were constructed and microbial community assemblies were determined by analysis of a total of 801 unique clone sequences from all the sites. Operational Taxonomic Unit (OTU)--based analysis of the sequences revealed highly diverse communities in each of the reactors and the constructed wetland. A total of 32 phylotypes were identified with the dominant members affiliated to Clostridia (33%), Betaproteobacteria (10%), Bacteroidia (10%), Deltaproteobacteria (9%) and Gammaproteobacteria (6%). Sequences affiliated to the class Clostridia were the most abundant across all sites. The 801 sequences were assigned to 255 OTUs, of which 3 OTUs were shared among the clone libraries from all sites. The shared OTUs comprised 80 sequences belonging to Clostridiales Family XIII Incertae Sedis, Bacteroidetes and unclassified bacterial group. Significantly different communities were harbored by the anaerobic, aerobic and rhizosphere sites of the constructed wetland. Numerous representative genera of the dominant bacterial classes obtained from the different sample sites of the integrated system have been implicated in the removal of various carbon- containing pollutants of natural and synthetic origins. To our knowledge, this is the first report of microbial community structure in tannery wastewater treatment plant from Ethiopia.

Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms. Published version

International audience; Overcoming the problem of resistance to antiretroviral drugs (ARVs) in HIV-infected patients is a major issue in AIDS research today. Advances in genome sequencing have facilitated the identification of a growing number of individual genotypes. Hence, it is now possible to understand HIV drug resistance at the molecular level by considering the three-dimensional (3D) structural interactions between ARVs and the mutated viral proteins of patients. Therefore, identification of the critical interactions lost further to one or several HIV mutations, and consequently the modifications of other molecular factors, could be indicators to propose appropriate ARVs escaping the resistance. This paper introduces the HIV-PDI (Protein-Drug Interactions) resource designed to be a decision making tool to propose alternative ARVs against a particular mutated viral protein, and thus to provide a personalized antiretroviral treatment. The HIV-PDI was conceived to serve as an integrated resource for studying HIV drug resistance at the structural level of the protein-drug interaction, with a special emphasis on the active site of the HIV drug target. As a first step, we focus on the well documented protease and related drugs. The HIV-PDI includes clinical information on patients, resistance to given ARVs treatments, HIV proteins structures and mutations, HIV protein/ARV drugs and their 3D interactions. The HIV-PDI may be queried using multiple combinations of fields including protein, drug and treatment conditions and coupled to visualization/analysis tools of 3D Protein-Drug interactions. The HIV-PDI resource can be used in order to help understand the appearance of resistance and to promote further novel drug and treatment developments based on analyses of 3D pattern of protein-drug interactions. A web-based version of HIV-PDI is available at http://hiv-pdi.loria.fr.

International audience; The HIV-PDI resource was designed and implemented to address the problems of drug resistance with a central focus on the 3D structure of the target-drug interaction. Clinical and biological data, structural and physico-chemical information and 3D interaction data concerning the targets (HIV protease) and the drugs (ARVs) were meticulously integrated and combined with tools dedicated to study HIV mutations and their consequences on the efficacy of drugs. Here, the capabilities of the HIV-PDI resource are demonstrated for several different scenarios ranging from retrieving information associated with patients to analyzing structural data relating cognate proteins and ligands. HIV-PDI allows such diverse data to be correlated, especially data linking antiretroviral drug (ARV) resistance to a given treatment with changes in three-dimensional interactions between a drug molecule and the mutated protease. Our work is based on the assumption that ARV resistance results from a loss of affinity between the mutated HIV protease and a drug molecule due to subtle changes in the nature of the protein-ligand interaction. Therefore, a set of patients whose resistance to first line treatment was corrected by a second line treatment was selected from the HIV-PDI database for detailed study, and several queries regarding these patients are processed via its graphical user interface. Considering the protease mutations found in the selected set of patients, our retrospective analysis was able to establish in most cases that the first line treatment was not suitable, and it predicted a second line treatment which agreed perfectly with the clincian's prescription. The present study demonstrates the capabilities of HIV-PDI. We anticipate that this decision support tool will help clinicians and researchers find suitable HIV treatments for individual patients. The HIVPDI database is thereby useful as a system of data collection allowing interpretation on the basis of all available information, thus helping in possible decision-makings.

Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.

Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group of 38 participants. The final list of 20 issues includes topics spanning from the political (the regulation of genomic data, increased philanthropic funding and malicious uses of neurochemicals) to the environmental (crops for changing climates and agricultural gene drives). The early identification of such issues is relevant to researchers, policy-makers and the wider public.