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opencc-zeroJun 2024View details →

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Structural variation has been associated with genetic diversity and adaptation in diverse taxa. Despite these observations, it is not yet clear what their relative importance is for microevolution, especially with respect to known drivers of diversity, e.g., nucleotide substitutions, in rapidly adapting species. Here we examine the significance of structural variants (SVs) in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation within this species. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral non-pest individuals. We identify >200,000 SVs, which appear to be non-randomly distributed across the genome as they co-occur with transposable elements and genes. SVs intersect exons for a large proportion of gene annotations (~20%) and are associated with insecticide resistance, development, and transcription, most notably cytochrome P450 (CYP) genes. To understand the role that SVs might play in adaptation we measure allele frequencies of SVs for an additional 57 individuals, using whole genome resequencing data, representing pest and non-pest populations of North America. Incorporating multiple independent tests of significance using SNP data, we identify 14 positively selected genes that include SVs and SNPs of elevated frequency within the sampled pest lineages. Among these, four are associated with insecticide resistance. One of these genes, glycosyltransferase-13, is a duplicated gene enclosed within a structural variant that resides inside the CYP4g15 genic region. Both gene products have been observed to be co-induced during insecticide exposure. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.

opencc-by-4.0Dec 2018View details →

TAD-fusion score: discovery and ranking the contribution of deletions to genome structure

Datasets and code of the manuscript: Huynh L. & Hormozdiari F., TAD-fusion score: discovery and ranking the contribution of deletions to genome structure.

opencc-by-4.0Aug 2022View details →

Fig. 4 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 4. (continued).

opencc-by-4.0Aug 2022View details →

Fig. 3 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 3. The secondary structure of 22 tRNA in Platygaster robiniae.

opencc-by-4.0Sep 2024View details →

Whole-genome sequencing reveals contribution of rare and common variation to structural kidney and urinary tract malformations

Supplementary tables detailing analysis of whole-genome sequencing data from 992 patients with congenital anomalies of the kidneys and urinary tract (CAKUT).

opencc-by-4.0Sep 2024View details →

Genome-wide comparison reveals large structural variants in the cassava landraces Authors

Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava. We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.

opencc-by-4.0Nov 2024View details →

Evolutionary trends in the compositional structure of the SARS-CoV-2 genome during the pandemic

By computing a measure of compositional genome structure in random datasets of coronavirus genomes, we observed a long-term decreasing trend in this measure, accompanied by an increasing evolutionary rate.

opencc-zeroDec 2016View details →

Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the Atlantic coast of Brazil we test for the effects of paleodrainages caused by sea-level changes during the Pleistocene. Given that the paleodrainage properties differ along the Brazilian coast, we also evaluate whether estimated genetic diversity within paleodrainages can be explained by past riverine properties (i.e., area and number of rivers in a paleodrainage). Our results demonstrate that genetic structure between populations is not just highly concordant with paleodrainages, but that differences in the genetic diversity among paleodrainages correspond to the joint effect of differences in the area encompassed by, and the number of rivers, within a paleodrainage. Our findings extend the influence of current riverine properties on genetic diversity to those associated with past paleodrainage properties. We discuss how these findings may explain the inconsistent support for paleodrainages in structuring divergence from different global regions and the importance of taking into account past conditions for understanding the high species diversity of freshwater fish that we currently observe in the world, and especially in the Neotropics.

opencc-zeroFeb 2023View details →

Different waves of postglacial recolonisation and genomic structure of bank vole population in NE Poland

Previous studies indicated that in some species phylogeographic patterns obtained in analyses of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check if there was any discordance between mitochondrial and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in analyses of other genetic markers and functional genes. However, genome-wide SNP analyses revealed a more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as previously recognised in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for an insufficient amount of time to develop significant genetic differentiation.

opencc-by-4.0Mar 2023View details →

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

Structural variant calls, RepeatMasker annotations, and genome assemblies of diverse mouse genomes.

opencc-zeroMar 2023View details →

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

opencc-by-4.0Apr 2023View details →

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

ncVarPred-1D3D: The data used for testing the inconsistency among genome sequence, epigenetic profile, and later, to show its relation to 3D chromatin structure can be found in sanity_check_data.tar.gz. Some trained model for noncoding mutation effect prediction (mapping genome sequence to epigenetic profile) can be found in CNN_MLP, CNN_GCN, CNN_RNN_MLP, CNN_RNN_GCN.tar.gz. The trained model for pathogenic variants prediction can be found in fewshot_pathogenic_model.tar.gz.  The training data can be found in training_data.tar.gz. Some noncoding variant effects prediction results, e.g. eQTL and pathogenic variants, can be replicated using the data shared in ncVar_data.tar.gz.

opencc-zeroJul 2023View details →

Data from: Genomic diversity and geographical structure of the Pyrenean desman

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Iberian Peninsula. The species has recently experienced a strong decline and some of its populations are severely threatened with extinction. To help in the preservation of this species, it is critical to understand its genetic structure and main evolutionary units, as these may have specific local adaptations and could be of great conservation value. Sequencing reduced representation libraries (ddRAD) from 26 specimens selected from across its entire range, we obtained around 45,000 loci per specimen and 1185 single nucleotide polymorphisms. Heterozygosity varied substantially among individuals from different areas. Interestingly, specimens from the southeastern Pyrenees had some of the lowest proportions of heterozygous positions inferred from genome-wide data in mammals so far. In addition, we estimated a tree reflecting genomic divergence, performed a principal component analysis, and carried out a Bayesian analysis of the population structure. Combined evidence supported the existence of five distinct genomic clusters largely coincident with the main mountain ranges where the species occurs, with few specimens presenting relevant admixture levels. There was good correspondence between these populations and the mitochondrial lineages detected in a previous study, yet substantial differences in some areas demonstrate the importance of performing genomic analysis to reveal the whole population history. Although the analysis of further specimens is necessary to better characterize the distribution of the different evolutionary units, the distinctive geographical structure of this species revealed by the genomic data should be considered in future conservation plans.

opencc-by-4.0Apr 2023View details →

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed. The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.

opencc-by-4.0Aug 2023View details →

Dataset related to "CFH and CFHR structural variants in atypical Hemolytic Uremic Syndrome: Prevalence, genomic characterization and impact on outcome "

The upload consists of 2 excel files, including genetic and clinical data, and 6 power point files with western blot images. SMRT sequencing data are deposited in the EBI European Nucletide Archive; Accession number: PRJEB44176.

Genomic diversity and population structure of teosintes (Zea spp.) and its conservation implications

The wild species of the genus Zea commonly named teosintes, comprise nine different taxa, distributed from northern Mexico to Costa Rica. Although this genus of plants has been extensively studied from a morphological, ecogeographical and genetic point of view, most contributions have been limited to the study of a few populations and taxa. To understand the great variability that exists between and within teosinte species, it is necessary to include the vast majority of known populations. In this context, the objective of this work was to evaluate the diversity and genomic structure of 276 teosinte populations. Molecular analyzes were performed with 3,604 plants and with data from 33,929 SNPs. The levels of genetic diversity by taxonomic group show a marked difference between species, races and sections, where the highest values of genomic diversity were found in ssp. parviglumis and ssp. mexicana. The lower values were obtained for the Luxuriantes section as well as ssp. huehuetenagensis of the section Zea. The results of the structure show that there is a great genetic differentiation in all the taxonomic groups considered. For ssp. parviglumis and mexicana, which are the taxa with the largest number of populations, a marked genomic differentiation was found that is consistent with their geographic distribution patterns. These results showed a loss of diversity in several teosinte populations, making a strong case for further collection, and ex situ and in situ conservation. Also, this study highlights the importance of integrating genomic diversity and structure for the applications of conservation and management.

Genomic analysis of geographical structure and diversity in the capercaillie (Tetrao urogallus)

The capercaillie is widespread throughout the boreal forests of northern Eurasia but faces serious conservation challenges in the southernmost mountain ranges, where the populations are fragmented and some are critically endangered. To develop effective conservation strategies for these populations, it is essential to have information on both their genetic diversity and the genetic structure of the species. In this work, we used a reduced representation (ddRAD) genomic sequencing technique to analyze the genetic structure of the capercaillie across its European range and to assess the inbreeding levels in some of the most threatened populations. Our population structure analysis suggested the existence of two evolutionarily significant units, one formed by the two populations from the Iberian Peninsula and the other by the populations from the rest of Europe. Genetic diversity showed a significant decrease in the Iberian populations with respect to the other European populations. An isolation-with-migration model supported these results and allowed us to estimate the parameters of the population tree. The inbreeding coefficients estimated for the Iberian capercaillies showed relatively low levels in the Pyrenees. However, some individuals with very high inbreeding values were detected in the Cantabrian Mountains, suggesting that some of its subpopulations are substantially isolated. The population structure results and the genomic monitoring method we used to assess inbreeding levels may be crucial for the conservation and recovery of the most endangered capercaillie populations.

Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific

The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S. viridula, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S. zebrina, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S. zebrina, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species.

Data from: Genomic architecture drives population structuring in Amazonian birds

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct general patterns of diversification in species that co-occur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate how inferring spatial patterns of diversification are sensitive to genomic architecture.