The evolution of SARS-CoV-2 Markov, Peter V; Ghafari, Mahan; Beer, Martin ...
Nature reviews. Microbiology,
06/2023, Volume:
21, Issue:
6
Journal Article
Peer reviewed
Open access
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has ...resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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IMTLJ, IZUM, KILJ, KISLJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
Summary
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, ...which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group‐, species‐ and accession‐specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non‐synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single‐nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20‐fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self‐incompatible wild species, while facultative and autogamous self‐compatible species display a lower heterozygosity level. Using whole‐genome SNP information for maximum‐likelihood analysis, we achieved complete tree resolution, whereas maximum‐likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Neopyropia yezoensis is a commercially important seaweed that has been subjected to industrial cultivation for more than six decades, making it a longstanding and economically valuable marine ...resource. However, there is a paucity of genomic information on its genetic structure and underlying domestication patterns. We examined 124 N. yezoensis samples collected from China and Japan, and identified 1,004,593 high-quality single-nucleotide polymorphisms (SNPs). Our results indicated that the genetic background of the cultivated population in China is complex, with evidence of germplasm mixing within the same cultivation area. We identified the genomic signatures and SNP hotspots of domestication related to growth, reproductive regulation, and improved stress resistance, thereby highlighting potential target genes for future nori breeding programs. Finally, two SNP loci, which are significantly associated with length, were identified through a genome-wide association study and were located within the region of selective sweeps in cultivated populations. Functional analysis indicated that one of the SNP loci might be involved in the regulation of flavin metabolism and transport. Our results will help elucidate the genetic diversity and evolutionary history of nori, and guide future breeding and conservation strategies.
•The cultivated population of N. yezoensis in China exhibits multiple genetic origins.•Artificial selective sweeps mostly occur in regions with low GC content and containing genes closely related to traits.•GWAS and selective sweep analysis jointly identified two SNPs associated with length-related traits.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Human cytomegalovirus (HCMV) glycoproteins H and L (gH/gL) can be bound by either gO or the UL128 to UL131 proteins (referred to here as UL128-131) to form complexes that facilitate entry and spread, ...and the complexes formed are important targets of neutralizing antibodies. Strains of HCMV vary considerably in the levels of gH/gL/gO and gH/gL/UL128-131, and this can impact infectivity and cell tropism. In this study, we investigated how natural interstrain variation in the amino acid sequence of gO influences the biology of HCMV. Heterologous gO recombinants were constructed in which 6 of the 8 alleles or genotypes (GT) of gO were analyzed in the backgrounds of strains TR and Merlin (ME). The levels of gH/gL complexes were not affected, but there were impacts on entry, spread, and neutralization by anti-gH antibodies. AD169 (AD) gO (GT1a) referred to here as ADgO(GT1a) drastically reduced cell-free infectivity of both strains on fibroblasts and epithelial cells. PHgO(GT2a) increased cell-free infectivity of TR in both cell types, but spread in fibroblasts was impaired. In contrast, spread of ME in both cell types was enhanced by Towne (TN) gO (GT4), despite similar cell-free infectivity. TR expressing TNgO(GT4) was resistant to neutralization by anti-gH antibodies AP86 and 14-4b, whereas ADgO(GT1a) conferred resistance to 14-4b but enhanced neutralization by AP86. Conversely, ME expressing ADgO(GT1a) was more resistant to 14-4b. These results suggest that (i) there are mechanistically distinct roles for gH/gL/gO in cell-free and cell-to-cell spread, (ii) gO isoforms can differentially shield the virus from neutralizing antibodies, and (iii) effects of gO polymorphisms are epistatically dependent on other variable loci.
Advances in HCMV population genetics have greatly outpaced understanding of the links between genetic diversity and phenotypic variation. Moreover, recombination between genotypes may shuffle variable loci into various combinations with unknown outcomes. UL74(gO) is an important determinant of HCMV infectivity and one of the most diverse loci in the viral genome. By analyzing interstrain heterologous UL74(gO) recombinants, we showed that gO diversity can have dramatic impacts on cell-free and cell-to-cell spread as well as on antibody neutralization and that the manifestation of these impacts can be subject to epistatic influences of the global genetic background. These results highlight the potential limitations of laboratory studies of HCMV biology that use single, isolated genotypes or strains.
By using 16 simple sequence repeat (SSR) markers, the genetic relatedness of 21 exceptional walnut genotypes was assessed. A significant degree of genetic diversity was observed within a given ...population, as indicated by the number of alleles per locus ranging from 2 to 4. WGA-1, WGA-4, and WGA-79 contained the greatest number of alleles (4), followed by WGA-118, WGA-202, and WGA-42. Conversely, WGA-27, WGA-69, and WGA-32 contained the fewest alleles. The range of the PIC value was 0.11 to 0.38. Using model-based cluster analysis, all genotypes were categorized into two primary clusters according to the UPGMA dendrogram, with varying degrees of sub-clustering. All the genotypes were categorized into six genetically distant subpopulations. The genotypes were genetically distinct but had variable degrees of admixture. The anticipated heterozygosity at a specific locus ranged from 0.563 to 0.741. Additionally, population differentiation (Fst) ranged between 0.176 and 0.261. These findings highlight the importance of considering germplasm diversity in walnut breeding programs and conservation efforts aimed at enhancing walnut cultivation in the region. Overall, this study contributes to our understanding of walnut genetic diversity in the Northwestern Himalayan region of Jammu and Kashmir and informs future breeding and conservation strategies.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Summary The influence of local habitat characteristics and landscape barriers on the distribution of species and genetic diversity remains poorly known. We tested for differences in turnover and ...total diversity in aquatic insect assemblages among headwater and mid-order reaches, two habitats presumably differing in their connectivity between catchments. The genus Hydropsyche (Trichoptera) includes 17 species in the eastern Iberian Peninsula and northern Morocco. Cytochrome c oxidase subunit I (cox1) gene was sequenced for Hydropsyche assemblages at 38 headwater sites and 12 mid-order sites. Local species and intraspecific genetic diversity and differentiation among populations were measured. A total of 231 cox1 sequences resulted in 83 unique haplotypes that clustered into 19 genetic species entities. We find that alpha-diversity did not differ between headwater and mid-order habitats at species and genetic levels, but total species numbers and intraspecific genetic diversity (gamma-diversity) were higher for headwater than for mid-order or lowland clades, due to greater turnover among sites (beta-diversity). The study revealed lineage-specific evolutionary responses to different river zones, presumably because of differences in the strength of landscape barriers. The multispecies community genetic approach provides a comprehensive picture of diversity patterns in Hydropsyche, as it links habitat heterogeneity and dispersal limitations to genetic structure and lineage diversification. PUBLICATION ABSTRACT
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, ...plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.
•Genetic erosion during domestication and modern breeding programs has led to reduce the genetic diversity of wheat.•Genetic structure of wheat can be improved through genetic enrichment by diversifying allelic combinations.•Tetraploid wheat subspecies are an excellent gene pool for improving tolerance to biotic and abiotic stresses.•Utilizing genes from tetraploid wheat subspecies provide great potential for increasing grain yield and quality of durum wheat.•Synthetic hexaploid wheat is an effective genetic resource to transfer important genes from wild relatives to common wheat.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background: The goat population of Andhra Pradesh and Telangana states is about five million, respectively. The goats of these two states lack phenotypic uniformity. But it is not known whether these ...populations have any genetically uniform group that can be registered as a breed. The study was undertaken to explore possibility of any potential new goat germplasm.Methods: Study was carried out at ICAR-NBAGR during 2017-19. Genetic diversity and differentiation was evaluated by using 22 microsatellite markers in three goat populations: Telangana Black (TB, n=26), Telangana Mixed (TM, n=49) and one Andhra Pradesh goat population (AP, n=45). Their genetic differentiation was compared with that of geographically closely distributed registered breeds viz. Bidri (n=28) and Nandidurga (n=48) of Karnatka and Ganjam (n=48) of Odisha. Result: The mean allele frequency observed was 6.59 (TB), 7.27 (TM) and 8.36 (AP). Expected number of alleles varied from 3.33 in (TB) to 3.69 in AP goats. Observed heterozygosity was lowest in the TM (0.474) followed by TB (0.504) and was highest in the AP goats (0.569). AP goat population had 6.3% heterozygote deficiency, whereas, both TB (15.4%) and TM (17.5%) had very high inbreeding coefficients. A total of 344 alleles were detected across the 22 loci in six goat groups. F-statistics, the pair-wise Nei’s genetic distance, assignment test and Baysian approach suggested that AP goats are distinct from two Telangana goat populations as well as from the other geographically closely related registered goat breeds. Genetic bottleneck analysis indicated the absence of any detectably large, recent genetic bottleneck in AP population. Altogether, the study identified Andhra Pradesh (AP) goats to be a new potential goat germplasm of India.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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![Higher [beta]- and [gamma]-...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0046-5070/small "Higher [beta]- and [gamma]-diversity at species and genetic levels in headwaters than in mid-order streams in Hydropsyche (Trichoptera)")
