In the original publication [...].

IMPORTANCE:Protozoan blood parasites, including Trypanosoma evansi, Theileria annulata, and Babesia spp., remain major constraints to livestock health and productivity across the Middle East and North Africa (MENA). Disease control relies heavily on a limited number of chemotherapeutic agents that have been used for decades, raising concern about declining efficacy and emerging drug resistance. OBSERVATIONS:This review synthesized and critically evaluated field, experimental, and molecular evidence of antiparasitic drug resistance in major protozoan blood parasites of livestock in the MENA region. A narrative review was conducted using major scientific databases to identify peer-reviewed studies published between January 2000 and December 2025. Eligible studies reported treatment outcomes, experimental drug sensitivity, or molecular resistance markers in T. evansi, T. annulata, or Babesia spp. Evidence was organized by parasite species and evidence type; meta-analysis was not performed due to heterogeneity. The most consistent evidence of confirmed drug resistance was found for T. annulata, where buparvaquone treatment failure is repeatedly associated with mutations in the cytochrome-b and TaPIN1 genes across multiple MENA countries. For trypanosomosis, recurrent field failures and experimental resistance to diminazene and isometamidium are reported, but validated molecular markers for T. evansi remain unavailable. In babesiosis, reported outcomes indicate variable or incomplete responses to imidocarb and diminazene, reflecting functional treatment failure rather than confirmed genetic resistance. CONCLUSIONS AND RELEVANCE:A clear mismatch exists between widespread field observations and limited molecular confirmation. Strengthened surveillance, standardized efficacy trials, rational drug use, and integrated parasite-control strategies are urgently needed in the MENA region.

African zebu cattle (Bos indicus) exhibit remarkable adaptation to extreme thermal conditions, yet the genomic bases of this resilience are not fully elucidated. Ethiopia provides a unique natural setting where closely related zebu populations have divergently adapted to hot-arid (DHETZ) and hot-humid (HHETZ) climates. In this study, we performed whole-genome sequencing of 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans ( iHS , Hp , XP-EHH , and XP-CLR ), we identified distinct and shared selection signatures between DHETZ and HHETZ cattle. Ethiopian zebu closely clustered with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. Although DHETZ and HHETZ cattle exhibited minimal genetic differentiation, reflecting their shared ancestry, each group displayed unique selection signals. DHETZ cattle showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling (e.g., SESN2 , DNAJC8 , GRPEL2 , ABLIM3 , and AFAP1L1 ). In contrast, HHETZ cattle displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition (e.g., MYD88 , PRKACA , PRKACB , and WIF1 ). Several genes, including VEGFC , TNIP3 , and DMXL2 , were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. These findings reveal a dual pattern of genomic adaptation: while core heat-response pathways are shared, population-specific signatures reflect distinct metabolic and vascular strategies for coping with arid versus humid heat stress. This study provides novel insights into the genomic architecture of environmental adaptation in tropical cattle and offers valuable markers for breeding climate-resilient livestock. ### Competing Interest Statement The authors have declared no competing interest.

Abstract Indigenous chickens play a critical role in food security and climate resilience in smallholder systems, yet their genomic diversity and adaptive potential remain insufficiently characterised. This study employed low-pass whole-genome sequencing (LP-WGS; 0.2–1.99×) to investigate genomic diversity, population structure, inbreeding and candidate environment-associated genomic variation in 33 chickens from highland, midland, and lowland agroecologies in the Tigray region of northern Ethiopia. After imputation and stringent filtering, 23.4 million high-confidence SNPs were retained, including ~ 17% novel variants, indicating substantial uncharacterised genetic diversity in these populations. SNP density (13.8 ± 8.6 SNPs/kb) was comparable to values reported from high-coverage Ethiopian chicken datasets, demonstrating the suitability of LP-WGS for population genomics in resource-limited settings. Marked differences in genomic diversity were observed among ecotypes: midland chickens showed the highest nucleotide diversity (π = 0.00267), followed by lowland (π = 0.00233), whereas highland chickens showed the lowest diversity (π = 0.00203) and elevated genomic inbreeding (F ROH and F HOM ≈ 0.18). Population structure analyses revealed clear genetic separation among ecotypes. PCA (13.91% variation explained) distinguished lowland chickens along PC1 and separated highland from midland along PC2, while ADMIXTURE and F ST patterns supported three major ancestral genomic backgrounds. Functional annotation of private missense variants uncovered distinct adaptive signatures reflecting the contrasting agroecological conditions. Highland chickens showed enrichment of candidate genes potentially involved in physiological processes relevant to high-altitude environments, including cold response, angiogenesis, cardiovascular regulation and metabolic homeostasis (eg., PARP1 , ACOX2 , ITGB3 , EDNRB , SOX8 , and SOX10 ). Midland chickens exhibited candidate signals of selection in genes with known roles in innate antiviral immunity, bacterial defence and inflammatory regulation (eg., BAK1 , CLSTN1 , CYSLTR1 , CYSLTR2 , CXCR7 , GIPR , DSCAM , GDAP1 , TLR3 , TLR4 , TLR7 , IFIH1 , ADORA1 , EPHB1 , and TMPRSS2 ). Lowland chickens displayed candidate variants associated with heat-stress response, DNA damage repair, oxidative balance and cardiovascular support under extreme temperatures (e.g., MLH1 , BDKRB1 , GPR19 , FLT1 , CCL18 , TGM2, and RAMP3 ). Overall, the results indicate substantial genomic differentiation among ecotypes and suggest candidate environment-associated genetic divergence across Tigray’s diverse agroecological zones. These populations may represent important reservoirs of adaptive genetic variation for climate-resilient poultry breeding, warranting further functional validation and conservation-oriented management.

African zebu cattle (Bos indicus) exhibit remarkable adaptations to extreme thermal conditions, yet the genomic basis of this resilience remains incompletely characterized. Ethiopia provides a unique natural setting in which closely related zebu populations have adapted divergently to dry-hot (DHETZ) and humid-hot (HHETZ) climates. In this study, we reanalyzed publicly available whole-genome sequencing datasets from 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans (iHS, Hp, XP-EHH, and XP-CLR), we identified distinct and shared selection signatures between DHETZ and HHETZ. We detected 33.7 million and 34.2 million biallelic autosomal SNPs in DHETZ and HHETZ, respectively. Ethiopian zebu clustered closely with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. DHETZ and HHETZ exhibited very low genetic differentiation (FST = 0.0063), consistent with their shared ancestry; however, each group displayed unique selection signals. In DHETZ, iHS and Hp detected 298 and 113 candidate regions, respectively, whereas in HHETZ, they detected 244 and 138 regions, respectively. Cross-population XP-EHH and XP-CLR analyses identified 163 and 227 divergent regions between DHETZ and HHETZ, respectively. Integration of the four selection scans identified 19 high-confidence candidate regions in DHETZ and 13 in HHETZ. DHETZ showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling, including SESN2, DNAJC8, GRPEL2, ABLIM3, and AFAP1L1. In contrast, HHETZ displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition, including MYD88, PRKACA, PRKACB, and WIF1. Several genes, including VEGFC, TNIP3, and DMXL2, were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. The shared VEGFC signal and the HHETZ-specific WIF1 signal may indicate a distinct vascular regulatory mechanism in the dry-hot and humid-hot environments. Our results reveal a dual pattern of genomic adaptation in Ethiopian zebu cattle and provide candidate loci for future validation and climate-resilient livestock breeding.

IntroductionThis study presents a comprehensive analysis of the complete mitochondrial genomes of Fasciola gigantica isolated from cattle, sheep, and goats in Sudan, aiming to provide new insights into genetic diversity, evolutionary dynamics, and host adaptation.MethodsMitochondrial genomes were sequenced using high-throughput Illumina MiSeq technology, yielding sequences of 14,483 bp, slightly longer than the reference genome (14,478 bp). A sliding window analysis was conducted to assess nucleotide diversity, and phylogenetic analyses were performed using complete mitochondrial sequences, including and excluding non-coding regions.ResultsKey genetic variations were observed, including a non-canonical start codon (GTG) in the ND5 gene and an alternative stop codon (TAA) in ND4. Length polymorphisms in ND4L and cox1 suggested potential mitochondrial efficiency adaptations. Non-coding regions showed minor length differences, with the long non-coding region extending by 20 bp and the short by 4 bp. Sliding window analysis identified ND4 and ND5 as the most variable genes, while cox1, nd1,andcox2 were the most conserved. Phylogenetic analysis showed distinct clustering of Sudanese F. gigantica isolates with strong bootstrap support. Excluding the D-loop preserved phylogenetic structure, while D-loop-specific analysis revealed high variability, particularly in the sheep isolate.DiscussionThese findings highlight significant genetic variation and evolutionary divergence among F. gigantica isolates in Sudan. The observed diversity, particularly within non-coding and variable coding regions, underscores the influence of regional evolutionary pressures and host-associated adaptations. This work enhances understanding of F. gigantica’s genetic landscape and supports the development of more targeted molecular surveillance and control strategies for fascioliasis in endemic regions.

Introduction Domestic chickens primarily descended from the wild red junglefowl, play a crucial role in global egg and meat production. China hosts diverse indigenous chicken populations that have adapted to various environmental conditions, including high-altitude with hypoxic and ultraviolet radiation stress. Method We analyzed whole-genome sequences of 118 birds from five Indigenous Chinese chicken populations and 295 chicken genomes from publicly available databases to identify genomic diversity, admixture, and selection signatures of chickens adapted to high-altitude environments. Selection signatures were identified using nucleotide diversity (π), Tajima’s D, XPEHH, and XP-CLR, selection scan methods. Results We observed a reduction in genetic diversity and historical declines in effective population size in high-altitude chicken, suggesting ongoing selection pressures shaping these populations. Selection scans identified nine genomic regions under strong positive selection, enriched for genes associated with hypoxia and ultraviolet radiation. Notably, five genes (TPK1, BAZ2B, MARCHF7, LLGL2, and RCAN3) were repeatedly detected across multiple selection signature analyses. RNA-seq analysis further confirmed the differential expression of these genes in the lung and heart tissues of chickens adapted to high and low altitudes, reinforcing their role in physiological adaptation to hypoxic environments. Altitude adaptation is driven by the selection of genes involved in oxygen metabolism, cellular stress response, and energy regulation. Conclusion Our study provides compelling genetic evidence for differentiation between high and low and high-altitude Chinese chicken populations. These findings also ensure our understanding of local adaptation in poultry and establish a genomic framework for breeding strategies to improve environmental resilience to altitude-related stressors.

Camels (Camelus dromedarius and Camelus bactrianus) are indispensable to the economy and culture of arid and semi-arid regions, providing milk, meat, transportation, and labor while demonstrating remarkable adaptations to extreme environments. Recent advances in camel genomics have unraveled key genetic insights related to diversity, physiological adaptation, and productivity traits. However, translating these genomic discoveries into practical applications remains limited by a critical gap in phenotypic data, standardized trait recording, and robust pedigree infrastructure essential foundations for implementing genomic selection (GS) effectively. The lack of high-density SNP arrays, variable linkage disequilibrium patterns, and incomplete genome assemblies further complicate efforts to identify causal variants, cautioning against overinterpreting GWAS results. This review provides a comprehensive analysis of camel genomics, emphasizing key genetic markers associated with growth, meat and milk production, coat color, athletic performance, environmental adaptation, cartilage integrity, and behavioral traits. Additionally, it highlights the importance of modeling genotype-by-environment interactions (G × E) and adopting advanced statistical approaches, such as random regression and reaction norm models, to capture complex trait architectures. Drawing lesson from other livestock, we propose a strategic roadmap that includes the development of high-density SNP arrays, improved genome assemblies, standardized trait recording, and establishment of large, connected training populations. International collaboration through a camel genomics consortium is essential to harmonize data, enhance genetic connectedness, and enable multi-environment evaluations. Addressing these research gaps will facilitate the development of precision breeding, climate-resilient livestock strategies, and sustainable conservation initiatives, ensuring that camels continue to thrive amid growing environmental and economic challenges.

IMPORTANCE:Vector-borne hemoparasitic diseases, such as Theileria, Babesia, Trypanosoma, Leishmania, and Anaplasma, pose significant constraints to livestock production, particularly in Africa and other tropical regions. These infections cause considerable economic losses from mortality, decreased productivity, and the high costs of treatment and control efforts. OBSERVATIONS:Resistance to hemoparasitic infections in livestock is strongly influenced by the genetic factors of the host. The key host genes involved in immune responses (e.g., BoLA-DRB3 and TLR4), oxidative stress defense (SOD2 and GPX1), drug metabolism (ABCB1 and CYP3A4), and ectoparasite resistance (MC1R and MHC) have been identified as contributors to resistance phenotypes. On the parasite side, the genes responsible for immune evasion (VSG and AP2), drug resistance (MDR1 and CYTB), and host cell invasion (AMA1 and HSP90) play pivotal roles in infection persistence and treatment failure. The advances in genomic and transcriptomic tools, including genome-wide association studies, CRISPR, and multi-omics profiling, have enhanced the understanding of these host-parasite interactions and enabled identification of the molecular markers for resistance traits. CONCLUSIONS AND RELEVANCE:Advanced genetic resistance offers a sustainable, long-term solution to managing vector-borne parasitic infections in livestock. The integration of resistance-associated markers into selective breeding programs, coupled with genome editing and real-time surveillance, can improve livestock resilience. Aligning these efforts with One Health strategies and collaborative genomic initiatives will be essential for achieving effective, regionally adapted disease control.

The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasive ranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra. Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.

Abstract Complete mitochondrial (mt) genomes are increasingly being used as molecular markers for investigating phylogenetic relationships. We sequenced the complete mt genome of the Fasciola gigantica of 16 samples from cattle, sheep and goats from Sudan using Illumina MiSeq platform. The complete mt genome of F. gigantica was 14,483 bp in length. Its genome is circular, and consists of 36 genes, including 12 protein-coding genes, 2 subunit ribosomal RNA genes (rRNA), and 22 genes for tRNA. The start and stop codons of the12 protein-coding genes are ATG and TAG respectively, which are identical to reference mt genomes except for the ND5 the start codon GTG and the stop codon of the ND4 which was TAA. Additionally, the lengths of the the12 protein-coding genes were identical in 10 genes, however, the ND4L of the reference was 12 bp longer with 273 bp as compared to the Sudan isolates which was 261 bp long and COX1 in the reference was 9 bp shorter which was 1,533 bp long as compared to Sudan isolates which 1,542 bp long. In contrast, the non-coding regions differed by 20 bp and 4 bp length in the long and the short non-coding regions of Sudan isolates. Nucleotide variability in the mt genome among F. gigantica from Sudan is quite different from the reference as revealed by the sliding window analysis. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that all F. gigantica from Sudan clustered separately from the available F. gigantica. More interestingly, based on stem-loop (non-coding regions) it revealed better resolution on how the evolutionary process has affected host specificity and in particular for the sheep and goats. It is concluded that these novel complete mt genomes of F. gigantica from different host species provide additional genetic markers for studying epidemiology, population genetics, and phylogeographics of F. gigantica, as well as for understanding interplay and the host species.

Introduction The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar-DRB1 , directly influences the specturm of presented antigens impacting immune responses and disease susceptability. Understanding the allelic diversity of Ovar-DRB1 gene in Sudan Desert Sheep (SDS) is essential for uncovering the genetic basis of immune responses and disease resistance, given the the breeds significance in Sudan's unique environment. Methods Utilizing Targeted Next-Generation Sequencing (NGS) we explore allelic diversity in Ovar-DRB1 gene within SDS. Successfully ampliying and and sequencing the second exon of this gene in 288 SDS samples representing six breeds provided a comprehensive allelic profile, enabling a detalied examination of the gene's genetic makeup. Results We identifed forty-six alleles, including four previously unreported, enrichness the genetic diversity of SDS breeds. These alleles exhibiting non-uniform distribution, varying frequencies across breeds, indicating a breed-specific genetic landscape. Certain alleles, known and novel, show higher frequencies in specific populations, suggesting potential associations with adaptive immune responses. Identifying these alleles sets the stage for investigating their functional roles and implications for disease resistance. Genetic differentiation among SDS breeds, as indicated by F ST values and clustering analyses, highlights a unique genetic makeup shaped by geographic and historical factors. These differentiation patterns among SDS breeds have broader implications for breed conservation and targeted breeding to enhance disease resistance in specific populations. Conclusion This study unveils Ovar-DRB1 gene allelic diversity in SDS breeds through targeted NGS and genetic analyses, revealing new alleles that underscore the breeds’ unique genetic profile. Insights into the genetic factors governing immune responses and disease resistance emerge, promising for optimization of breeding strategies for enhanced livestock health in Sudan’s unique environment.

Fasciola gigantica is a widespread parasite that causes neglected disease in livestock worldwide. Its high transmissibility and dispersion are attributed to its ability to infect intermediate snail hosts and adapt to various mammalian definitive hosts. This study investigated the variation and population dynamics of F. gigantica in cattle, sheep, and goats from three states in Sudan. Mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) genes were sequenced successfully to examine intra and interspecific differences. ND1 exhibited higher diversity than COI, with 15 haplotypes and 10 haplotypes, respectively. Both genes had high haplotype diversity but low nucleotide diversity, with 21 and 11 polymorphic sites for ND1 and COI, respectively. Mismatch distribution analysis and neutrality tests revealed that F. gigantica from different host species was in a state of population expansion. Maximum likelihood phylogenetic trees and median networks revealed that F. gigantica in Sudan and other African countries had host-specific and country-specific lineages for both genes. The study also indicated that F. gigantica-infected small ruminants were evolutionarily distant, suggesting deep and historical interspecies adaptation.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

The utilization of complete mitochondrial (mt) genomes as molecular markers for exploring phylogenetic relationships is increasingly prevalent. Here, we conducted sequencing of the complete mt genome of Fasciola gigantica from 16 samples sourced from cattle, sheep, and goats in Sudan, employing the Illumina MiSeq platform. The resultant mt genome of F. gigantica measured 14,483 bp in length, presenting a circular configuration and comprising 36 genes, including 12 protein-coding genes, 2 subunit ribosomal RNA genes (rRNA), and 22 transfer RNA genes (tRNA). Notably, the start and stop codons of the 12 protein-coding genes were consistently ATG and TAG, respectively, matching reference mt genomes, with the exception of the ND5 gene's start codon (GTG) and the ND4 gene's stop codon (TAA). While the lengths of ten protein-coding genes remained identical between the reference and Sudan isolates, variations were observed in ND4L and COX1. Specifically, the ND4L gene in the reference was 12 bp longer, measuring 273 bp compared to the Sudan isolates, which were 261 bp long. Conversely, COX1 in the reference was 9 bp shorter, measuring 1,533 bp, in contrast to the Sudan isolates, which were 1,542 bp long. These discrepancies highlight specific genomic differences between the reference and Sudan isolates of Fasciola gigantica, potentially indicative of evolutionary divergence or genetic adaptation within distinct populations. Evaluation of non-coding region lengths further revealed disparities between Sudan isolates and the reference. Sliding window analysis unveiled notable nucleotide variability within the mt genome of F. gigantica from Sudan compared to the reference. Phylogenetic analysis, based on concatenated amino acid sequences of all 12 protein-coding genes, depicted distinct clustering of F. gigantica from Sudan. Noteworthy insights into the evolutionary process affecting host specificity, particularly in sheep and goats, were gleaned from stem-loop analysis of non-coding regions. In conclusion, the novel complete mt genomes of F. gigantica from diverse host species serve as valuable genetic markers for investigating epidemiology, population genetics, phylogeography, and host-species interactions. .

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D - loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.

BACKGROUND:Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. RESULTS:We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. CONCLUSIONS:Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle.

Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic arboviral disease that poses a great threat to global health in the Old World, and it is endemic in Europe, Asia, and Africa, including Sudan. In this retrospective study, we reviewed previous epidemiological reports about the major epidemics of CCHF throughout Sudan between 2010 and 2020. During these epidemics, the infection of humans with Crimean-Congo hemorrhagic fever virus (CCHFV), the causative agent of CCHF, was diagnosed using qRT-PCR. We have identified 88 cases of CCHF, including 13 fatalities reported during five epidemics that occurred in 2010, 2011, 2015, 2019, and 2020. The two epidemics in 2010 and 2011 were by far the largest, with 51 and 27 cases reported, respectively. The majority of cases (78%) were reported in the endemic region of Kordofan. Here, we document that the first emergence of CCHFV in the Darfur region, West Sudan, occurred in 2010. We were not able to investigate outbreak dynamics through phylogenetic analysis due to the limited diagnostic capacity and the lack of sequencing services in the country. These findings call for establishing a genomic-based integrated One Health surveillance and response system for the early preparedness, prevention, and control of CCHF in the country.

Increases in arbovirus outbreaks in Sudan are vectored by Aedes aegypti, raising the medical importance of this mosquito. We genotyped 12 microsatellite loci in four populations of Ae. aegypti from Sudan, two from the East and two from the West, and analyzed them together with a previously published database of 31 worldwide populations to infer population structure and investigate the demographic history of this species in Sudan. Our results revealed the presence of two genetically distinct subspecies of Ae. aegypti in Sudan. These are Ae. aegypti aegypti in Eastern Sudan and Ae. aegypti formosus in Western Sudan. Clustering analysis showed that mosquitoes from East Sudan are genetically homogeneous, while we found population substructure in West Sudan. In the global context our results indicate that Eastern Sudan populations are genetically closer to Asian and American populations, while Western Sudan populations are related to East and West African populations. Approximate Bayesian Computation Analysis supports a scenario in which Ae. aegypti entered Sudan in at least two independent occasions nearly 70–80 years ago. This study provides a baseline database that can be used to determine the likely origin of new introductions for this invasive species into Sudan. The presence of the two subspecies in the country should be consider when designing interventions, since they display different behaviors regarding epidemiologically relevant parameters, such as blood feeding preferences and ability to transmit disease.