Amid the global challenges posed by the COVID-19 pandemic, unraveling the genomic intricacies of SARS-CoV-2 became crucial. This study explores viral evolution using an innovative high-throughput ...next-generation sequencing (NGS) approach. By taking advantage of nasal swab and mouthwash samples from patients who tested positive for COVID-19 across different geographical regions during sequential infection waves, our study applied a targeted enrichment protocol and pooling strategy to increase detection sensitivity. The approach was extremely efficient, yielding a large number of reads and mutations distributed across 10 distinct viral gene regions. Notably, the genes Envelope, Nucleocapsid, and Open Reading Frame 8 had the highest number of unique mutations per 1000 nucleotides, with both spike and Nucleocapsid genes showing evidence for positive selection. Focusing on the spike protein gene, crucial in virus replication and immunogenicity, our findings show a dynamic SARS-CoV-2 evolution, emphasizing the virus-host interplay. Moreover, the pooling strategy facilitated subtle sequence variability detection. Our findings painted a dynamic portrait of SARS-CoV-2 evolution, emphasizing the intricate interplay between the virus and its host populations and accentuating the importance of continuous genomic surveillance to understand viral dynamics. As SARS-CoV-2 continues to evolve, this approach proves to be a powerful, versatile, fast, and cost-efficient screening tool for unraveling emerging variants, fostering understanding of the virus's genetic landscape.
Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species' survival and ...adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes.
In this work, we improved the genome assemblies of the three Old World camel species - domestic dromedary and Bactrian camel, and the two-humped wild camel - via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex.
The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with a combined role of population history and differential exposures to pathogens, and consequent different selective pressures.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Dromedaries are an important livestock, used as beasts of burden and for meat and milk production. However, they can act as an intermediate source or vector for transmitting zoonotic viruses to ...humans, such as the Middle East respiratory syndrome coronavirus (MERS-CoV) or Crimean-Congo hemorrhagic fever virus (CCHFV). After several outbreaks of CCHFV in the Arabian Peninsula, recent studies have demonstrated that CCHFV is endemic in dromedaries and camel ticks in the United Arab Emirates (UAE). There is no apparent disease in dromedaries after the bite of infected ticks; in contrast, fever, myalgia, lymphadenopathy, and petechial hemorrhaging are common symptoms in humans, with a case fatality ratio of up to 40%. We used the in-solution hybridization capture of 100 annotated immune genes to genotype 121 dromedaries from the UAE tested for seropositivity to CCHFV. Through univariate linear regression analysis, we identified two candidate genes belonging to the innate immune system:
and
These genes have important functions in the host defense against viral infections and in stimulating natural killer cells, respectively. This study opens doors for future research into immune defense mechanisms in an enzootic host against an important zoonotic disease.
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this ...widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.
The recent SARS-CoV-2 pandemic has refocused attention to the
, only eight years after the emergence of another zoonotic
, the Middle East respiratory syndrome coronavirus (MERS-CoV). While the wild ...source of SARS-CoV-2 may be disputed, for MERS-CoV, dromedaries are considered as source of zoonotic human infections. Testing 100 immune-response genes in 121 dromedaries from United Arab Emirates (UAE) for potential association with present MERS-CoV infection, we identified candidate genes with important functions in the adaptive, MHC-class I (
-like) and II (
-like), and innate immune response (
), and in cilia coating the respiratory tract (
). Some of these genes previously have been associated with viral replication in SARS-CoV-1/-2 in humans, others have an important role in the movement of bronchial cilia. These results suggest similar host genetic pathways associated with these
, although further work is required to better understand the MERS-CoV disease dynamics in both dromedaries and humans.
Dromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With ...increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.
Aim
The distribution of hares (Lepus spp.) in southern Europe was markedly different at the Last Glacial Maximum. Historical hybridization during range replacements led to high frequencies of mtDNA ...introgression from Lepus timidus into populations of three other species in northern Iberian Peninsula, even though L. timidus subsequently disappeared from the region. We use palaeontological records to provide new insights on the biogeographic history of these range replacements, combining ancient DNA and ecological niche modelling.
Location
Southern France.
Taxon
Hares (genus Lepus).
Methods
DNA was extracted from hare bones collected at Neolithic sites in southern France (5.5–7.5 thousand years before present; kyr bp) with uncertain species assignment. One mtDNA fragment was sequenced and 27 SNPs from 11 nuclear genes with species‐diagnostic information were genotyped. Distributions of L. granatensis, L. europaeus, and L. timidus were modelled using spatial and bioclimatic predictors, and the favourability function. Each model was transferred to 6 kyr bp and favourabilities were combined to determine the species with the highest environmental favourability in each sampled locality.
Results
Ancient DNA analysis showed that the screened specimens belong to L. granatensis, a species presently confined to the Iberian Peninsula, but carried mtDNA haplotypes from L. timidus. Niche models show that L. granatensis achieved highest favourability in southern France 6 kyr bp reinforcing the molecular evidences.
Main conclusions
L. granatensis replaced L. timidus populations from Iberia to southern France, being present in this region 5.5 kyr bp. Subsequent westwards invasion of L. europaeus likely replaced these L. granatensis populations towards northern Iberia, establishing current ranges. Despite successive species replacements, introgressed mtDNA haplotypes from L. timidus mark the distribution of the species in northern Iberian Peninsula before it disappeared in the region. Characterizing complex biogeographic histories of interacting species is a key to understand processes that led to current distributions of genetic diversity.
Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of ...the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.
The combination of past climatic and stochastic dispersal events resulted in the contemporary pattern of species diversity and distribution in Africa. The Pleistocene glaciations and the cyclic ...contractions and expansions of major vegetation zones had deep effects on the distribution and evolution of African mammals. These events dictated the presence of unique biogeographic and climatic areas, making Africa a very special area for biodiversity studies. Despite Africa being generally rich in biodiversity, there is still information deficiency in the organisms that are present, and the diversity and taxonomy of the already described organisms. Additionally, arid regions are normally assumed as plain areas with difficult conditions to sustain life, and therefore with less biodiversity when compared to other climatic regions. However, deserts can be superb endemic species repositories due to the past climatic events, and the Saharan desert is one example. Moreover, the biogeographical intersection between the Palearctic and Afrotropical regions in the Mediterranean basin is considered a hotspot of biodiversity in North Africa. But most of the existing molecular studies on African biodiversity involve vertebrates with low dispersal activity while relevant information on organisms with relative dispersal ability, like hares (genus Lepus), is far from being achieved.From the 32 Lepus species, 6 are described in Africa. However, the existing studies on this complex genus in Africa were mainly based on evidence of morphology and/or palaeontology, which are limited sources of information, due to the large overlap of characteristics between species. This species classification is far from being well established, and specialists commonly diverge on the number of distinct hares present in Africa, species or subspecies, and their distributions. To clarify the population history of these African hares and consequently contribute to a proper taxonomical classification of these organisms, the identification of the distinct evolutionary entities and their phylogenetic relationships is fundamental. The use of molecular tools therefore appears promising to this end.Among the African hares, the cape hare (Lepus capensis) is one of the most controversial species. This is one of the most widespread hare species, occurring from Africa to China, with distinct features in different regions that lead to the identification of 80 subspecies. Also, its range distribution is overlapped with other hare species, mostly with L. microtis and L. saxatilis in Africa. However, the level of differentiation and divergence within the cape hare as it is currently classified along its broad distribution is unknown. In order to better understand the evolutionary history of African hares and provide valuable information to clarify its taxonomy and systematics, the population structure and phylogeographic patterns of the species was investigated, inferring the demographic history of the populations in light of the large-scale climatic fluctuations of the Pleistocene. This genetic diversity was in addition analyzed in the context of the putative neighboring species. For this, the broadest sampling scheme ever performed in L. capensis was designed, including both museum and field collected samples and comprising several populations across Africa, with a particular focus on Northwest Africa, and sequences of other 4 Lepusspecies. The molecular characterization was performed with 18 newly developed microsatellites and sequences of 1 mitochondrial DNA and 5 nuclear DNA loci.The results revealed strong biogeographic structuring at the genetic level, inferred from the microsatellite data using Bayesian clustering methods, and deep divergences based on both on mitochondrial DNA alone and on the set of sequences from 5 nuclear DNA loci, based on phylogenetic analyses.
PDF
