Genomic Structural Variation Research Articles

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

BackgroundCopy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta.ResultsA total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3).ConclusionsThis study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing.

Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes.

Copy number variations (CNVs) are genomic structural variants with potential functional and evolutionary effects on phenotypes. In this study, we report the identification and characterization of CNVs from the whole-genome resequencing data of two northernmost cattle breeds from Russia: the Yakut and Kholmogory cattle and their phylogenetically most related breeds, Hanwoo and Holstein, respectively. Comparisons of the CNV regions (CNVRs) among the breeds led to the identification of breed-specific CNVRs shared by cold-adapted Kholmogory and Yakut cattle. An investigation of their overlap with genes, regulatory domains, conserved non-coding elements (CNEs), enhancers, and quantitative trait loci (QTLs) was performed to further explore breed-specific biology and adaptations. We found CNVRs enriched for gene ontology terms related to adaptation to environments in both the Kholmogory and Yakut breeds and related to thermoregulation specifically in Yakut cattle. Interestingly, the latter has also been supported when exploring the enrichment of breed-specific CNVRs in the regulatory domains and enhancers, CNEs, and QTLs implying the potential contribution of CNVR to the Yakut and Kholmogory cattle breeds’ adaptation to a harsh environment.

Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout.

Structural variation in genomes, such as copy number variants (CNVs), is under scrutiny for its contribution to phenotypic expression and evolution. Regions of homozygosity (ROH) are ripe for phenotype-gene discovery. Determining the genes and related phenotypes within genomic regions is key to studying potential functional and phenotypic consequences. Because individuals have multiple CNVs and ROHs in their genome, identifying genomic regions that are phenotypically significant is challenging. GeneScout is a web-based tool that can be used to search genomic regions to display and filter the genes and their associated phenotypes within regions of interest. Phenotypes and their associated gene(s) can then be filtered to show only the genes with phenotypes that have a particular inheritance pattern and/or specific clinical feature(s). Phenotypes can then be selected to compare the clinical synopses side-by-side in Online Mendelian Inheritance in Man (OMIM® ).Additionally, two coordinate sets can be compared to determine either the regions of overlap or the unique regions (subtraction). The resulting coordinate ranges are displayed on the results page, and the results table displays only the genes and phenotypes present within the coordinate ranges. The interactive table includes gene-specific links to external resources such as ClinVar, ClinGen validity, ClinGen dosage, and gnomAD, and a diamond symbol next to the gene name indicates a gene that spans the start or end of a coordinate range. Searches and comparisons may be performed for coordinates in assemblies GRCh37 (hg19) and GRCh38 (hg38). The results page offers the option to liftover coordinates entered in GRCh37 to GRCh38 and updates the results table to display the gene content based on assembly GRCh38. The search coordinates and results table can be downloaded in a tab-delimited or Excel file. © 2022 Wiley Periodicals LLC. Basic Protocol: Searching GeneScout.

Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells.

The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.

EVOLUTIONARY PATTERNS OF GENOME SIZE AND CHROMOSOME NUMBER VARIATION IN BEGONIACEAE

Cytological data resources are crucial to the study and understanding of the evolution of complex taxa. Recent research on the genus Begonia L. has provided a robust phylogenetic background for the analysis of evolutionary patterns across the group and has established that Begonia is variable in genome size and chromosome number. This paper provides an overview of the genome structural variation present in Begonia and an updated chromosome number and genome size dataset for the genus. Chromosome numbers of more than 400 species are presented and discussed within their current taxonomic and phylogenetic context. A more complete chromosome number dataset is available for Neotropical and Asian Begonia sections than for those from Africa. The distribution of chromosome numbers across phylogenetic trees supports the idea of Begonia sections as natural groups, because most variation is found between sections rather than within them. Some larger Begonia clades were found to have larger chromosome number variation. Moreover, groups with the most variable chromosome numbers belong to some of the taxonomically complex or unresolved Begonia sections. Genome size variation was found not to correlate with changes in chromosome number. It suggests that Begonia genome dynamics are caused not only by large-scale duplications, rearrangements, and changes in ploidy levels but also by changes in the repetitive fraction of the genome, which probably cause changes in chromosome size. This could potentially play an important role in species radiations.

Comparative Genomic and Phylogenetic Analysis of Forty Gentiana Chloroplast Genomes.

Gentiana plants, which have great medicinal and ornamental value, are widely distributed in diverse habitats and have complex taxonomy. Here 40 Gentiana chloroplast genomes were used for comparative genomic analysis and divergence time estimation. The complete chloroplast genome of G. rhodantha was sequenced, assembled, and annotated. Comparative genomic and phylogenetic analysis were provided for variation analysis of Gentiana. Gentiana species satisfy the characteristics of intra-Sect conservation and inter-Sect variation in chloroplast genome structure and IR boundaries. All Gentiana Sects can be clustered into a single one and separated from each other; however, Ser. Apteroideae and Ser. Confertifoliae in Sect. Monopodiae are more closely related to Sect. Frigida and Sect. Cruciata, respectively. Gentiana has experienced two large gene loss events; the first, the collective loss of the rps16 gene at genus formation and the second, the collective loss of the ndh gene when Ser. Ornatae and Ser. Verticillatae completed their differentiation. Comparative genomic analysis support that Sect. Stenogyne and Sect. Otophora became the independent genera Metagentiana and Kuepferia. Seven divergence hotspot regions were screened based on Pi values, and could serve as DNA-specific barcodes for Gentiana. This study provides a further theoretical basis for taxonomic analysis, genetic diversity, evolutionary mechanism and molecular identification in Gentiana.

Evolutionary insights into porcine genomic structural variations based on a novel‐constructed dataset from 24 worldwide diverse populations

AbstractStructural variations (SVs) are important DNA polymorphisms that contribute to genetic diversity and evolution in humans, animals, and plants. In this study, we present a novel swine SV dataset of 79,919 deletions, 23,638 duplications, and 9333 inversions with average sequence depths of 24.1× from 24 varieties of worldwide pig populations, encompassing 305 individuals. Genotypes of SVs, particularly deletions, can accurately group individuals based on their population identity. We showed that exon‐covering deletions were subject to negative selection. Fixation index and differential allele frequency analysis identified highly differentiated SVs between European and Asian indigenous pigs, including deletions in NR6A1 and PLAG1, which are significantly associated with vertebrate numbers and growth performances, respectively. The growth‐enhancing allele at the deletion in PLAG1 was shared by European commercial pigs and Northern Chinese indigenous pigs including Laiwu and Min pigs, suggesting potential introgression from European commercial breeds into Chinese indigenous breeds. Moreover, we uncovered highly differentiated SVs in 139 genes between domesticated pigs and wild boars in Asia, temperature and altitude adaptation‐associated SVs in 41 genes, and population‐specific SVs in 718 genes. This study provides novel insights into the role of porcine SVs in domestication, environmental adaptation, and breed formation.

Influence of genomic structural variations and nutritional conditions on the emergence of quorum sensing-dependent gene regulation defects in Burkholderia glumae.

Bacteria often change their genetic and physiological traits to survive in harsh environments. To determine whether, in various strains of Burkholderia glumae, genomic diversity is associated with the ability to adapt to ever-changing environments, whole genomes of 44 isolates from different hosts and regions were analyzed. Whole-genome phylogenetic analysis of the 44 isolates revealed six clusters and two divisions. While all isolates possessed chromosomes 1 and 2, strains BGR80S and BGR81S had one chromosome resulting from the merging of the two chromosomes. Upon comparison of genomic structures to the prototype BGR1, inversions, deletions, and rearrangements were found within or between chromosomes 1 and/or 2 in the other isolates. When three isolates—BGR80S, BGR15S, and BGR21S, representing clusters III, IV, and VI, respectively—were grown in Luria-Bertani medium, spontaneous null mutations were identified in qsmR encoding a quorum-sensing master regulator. Six days after subculture, qsmR mutants were found at detectable frequencies in BGR15S and BGR21S, and reached approximately 40% at 8 days after subculture. However, the qsmR mutants appeared 2 days after subculture in BGR80S and dominated the population, reaching almost 80%. No qsmR mutant was detected at detectable frequency in BGR1 or BGR13S. The spontaneous qsmR mutants outcompeted their parental strains in the co-culture. Daily addition of glucose or casamino acids to the batch cultures of BGR80S delayed emergence of qsmR mutants and significantly reduced their incidence. These results indicate that spontaneous qsmR mutations are correlated with genomic structures and nutritional conditions.

Origins, genomic structure and copy number variation of snake venom myotoxins

Crotamine, myotoxin a and homologs are short peptides that often comprise major fractions of rattlesnake venoms and have been extensively studied for their bioactive properties. These toxins are thought to be important for rapidly immobilizing mammalian prey and are implicated in serious, and sometimes fatal, responses to envenomation in humans. While high quality reference genomes for multiple venomous snakes are available, the loci that encode myotoxins have not been successfully assembled in any existing genome assembly. Here, we integrate new and existing genomic and transcriptomic data from the Prairie Rattlesnake (Crotalus viridis viridis) to reconstruct, characterize, and infer the chromosomal locations of myotoxin-encoding loci. We integrate long-read transcriptomics (Pacific Bioscience's Iso-Seq) and short-read RNA-seq to infer gene sequence diversity and characterize patterns of myotoxin and paralogous β-defensin expression across multiple tissues. We also identify two long non-coding RNA sequences which both encode functional myotoxins, demonstrating a newly discovered source of venom coding sequence diversity. We also integrate long-range mate-pair chromatin contact data and linked-read sequencing to infer the structure and chromosomal locations of the three myotoxin-like loci. Further, we conclude that the venom-associated myotoxin is located on chromosome 1 and is adjacent to non-venom paralogs. Consistent with this locus contributing to venom composition, we find evidence that the promoter of this gene is selectively open in venom gland tissue and contains transcription factor binding sites implicated in broad trans-regulatory pathways that regulate snake venoms. This study provides the best genomic reconstruction of myotoxin loci to date and raises questions about the physiological roles and interplay between myotoxin and related genes, as well as the genomic origins of snake venom variation.

P-546 The structure of genome variations at CNV level differs in recurrent and sporadic pregnancy loss

Abstract Study question Whether the CNV load differs in fetal tissues of miscarriages from families with recurrent and sporadic pregnancy loss? Summary answer In RPL group duplications are more common than deletions, de novo variants than inherited ones. Pathogenic CNVs (dup16p11.2, del22q13, dupXq28) were found in both groups. What is known already Data on CNVs in tissues of miscarriages can be found in more than 24 articles. Altogether 7732 samples were analyzed by aCGH and NGS; 988 CNVs of uncertain clinical significance were found in 636 samples (8.2%). The origin was determined for 130 variants: 85 maternal (65.4%), 34 paternal (26.2%), 11 de novo (8.4%) CNVs. No aberration unambiguously associated with miscarriage was found so far. Comparative analysis of CNVs in family trios with recurrent and sporadic miscarriage may help to characterize structural genome variations associated with embryo lethality both from embryo and parental side. Study design, size, duration Identification of structural genome variations (SGV) at the CNV level was performed by aCGH-analysis for family trios: mother, father and fetal. Characteristics of SGV associated with embryo lethality included such parameters as CNV type (deletion/duplication) and its origin. It was assumed that the structure of genomic variability may differ in recurrent pregnancy loss (RPL) and sporadic pregnancy loss (SPL) both in embryonic tissues and in parents. Participants/materials, setting, methods Eleven family trios (7 RPL and 4 SPL) were included in the research. Standard G-banding was performed for all abortion samples to exclude aneuploidy. STR-haplotyping for the SRY gene was used to exclude maternal cell contamination. Finally all samples were analyzed for CNVs using SurePrint G3 Human CGH+SNP 4 × 180K microarrays (Agilent Technologies). Average gestation age was 7.9 weeks. Average maternal and paternal age was 30.8 and 30.5 years, respectively. Main results and the role of chance In seven and four embryos from RPL and SPL groups 110 and 60 CNVs were identified, respectively. In RPL, there was a tendency towards an increase in the frequency of duplications over deletions (72:38) in comparison to SPL (36:24) (p = 0.5). Duplications prevailed over deletions in five of seven embryos from RPL group; while there were two cases of each combination in SPL. One can suggest that some SPL cases can move into RPL group over time. De novo variants prevailed over inherited in the RPL group (76:43) and inherited prevailed in the SPL (32:28) (p < 0.05). This result allows to suggest that in cases with RPL there may be some common genetic/epigenetic factor predisposing to CNV generation either in primordial germ cells or during early blastomere cleavage. Among the inherited variants in the RPL group there were 24 maternal and 8 paternal CNVs, while in the SPL – 18 and 14 (p = 0.1). In both groups pathogenic CNVs associated with syndromes characterized by neurodevelopmental disorders (NDD) in children were found (del22q13, dupXq28 – in RPL group, dup16p11.2 – two cases in SPL). Presumably, such aberrations may explain a high risk of NDD in a child of a woman with RPL/SPL (PMID:30058166, PMID:33580539). Limitations, reasons for caution No one CNV unambiguously associated with pregnancy loss has been described so far. Possibly, total structural genome variations level should be considered as pathogenic factor for embryo development. There is no adequate algorithm of clinical significance CNV interpretation for the embryonic period. Wider implications of the findings Prenatal or preimplantation genetic testing should be considered if one of the parents is a carrier of CNV associated with microdeletion/microduplication syndrome. This study was supported by the Russian Science Foundation № 21-65-00017, https://rscf.ru/project/21-65-00017/. Trial registration number Russian Science Foundation № 21-65-00017

Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)

Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.

Genome-Wide Comparative Analysis of Transposable Elements by Matrix-TE Method Revealed Indica and Japonica Rice Evolution

Transposons (TEs) are known to change the gene expression and function, and subsequently cause plant speciation and evolution. Nevertheless, efficient and new approaches are required to investigate the role of TEs in the plant genome structural variations. Here, we reported the method named matrix-TE to investigate the differentiation of intact and truncated LTR/TEs comprehensively in Indica and Japonica rice throughout whole genomes with a special eye on centromeric regions. Six LTR/TE super-families were identified in both Indica and Japonica rice genomes, and the TE ORF references were extracted by phylogenetic analysis. Indica rice specific TE peak P-Gypsy and Japonica rice specific TE peak P-Copia were observed, and were further analyzed by Gaussian probability density function (GPDF) fit. The individual TE peak P-Gypsy was observed in centromeric regions of the Indica genome. By the matrix-TE method, the divergence of Indica and Japonica genomes, especially their centromeric regions, mainly resulted from the Ty3/Gypsy insertion events at 0.77 Mya. Our data indicate that the optimized matrix-TE approach may be used to specifically analyze the TE content, family evolution, and time of the TE insertions.

Bursts of Genomic Instability Potentiate Phenotypic and Genomic Diversification in Saccharomyces cerevisiae.

How microbial cells leverage their phenotypic potential to survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. Stochastic phenotype switching, a particularly fascinating adaptive approach observed in numerous species across the tree of life, introduces phenotypic diversity into a population through mechanisms which have remained difficult to define. Here we describe our investigations into the mechanistic basis of colony morphology phenotype switching which occurs in populations of a pathogenic isolate of Saccharomyces cerevisiae, YJM311. We observed that clonal populations of YJM311 cells produce variant colonies that display altered morphologies and, using whole genome sequence analysis, discovered that these variant clones harbored an exceptional collection of karyotypes newly altered by de novo structural genomic variations (SVs). Overall, our analyses indicate that copy number alterations, more often than changes in allelic identity, provide the causative basis of this phenotypic variation. Individual variants carried between 1 and 16 de novo copy number variations, most of which were whole chromosomal aneuploidies. Notably, we found that the inherent stability of the diploid YJM311 genome is comparable to that of domesticated laboratory strains, indicating that the collections of SVs harbored by variant clones did not arise by a chronic chromosomal instability (CIN) mechanism. Rather, our data indicate that these variant clones acquired such complex karyotypic configurations simultaneously, during stochastic and transient episodes of punctuated systemic genomic instability (PSGI). Surprisingly, we found that the majority of these highly altered variant karyotypes were propagated with perfect fidelity in long-term passaging experiments, demonstrating that high aneuploidy burdens can often be conducive with prolonged genomic integrity. Together, our results demonstrate that colony morphology switching in YJM311 is driven by a stochastic process in which genome stability and plasticity are integrally coupled to phenotypic heterogeneity. Consequently, this system simultaneously introduces both phenotypic and genomic variation into a population of cells, which can, in turn perpetuate population diversity for many generations thereafter.

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps.

The Hi-C technique has been shown to be a promising method to detect structural variations (SVs) in human genomes. However, algorithms that can use Hi-C data for a full-range SV detection have been severely lacking. Current methods can only identify interchromosomal translocations and long-range intrachromosomal SVs (>1 Mb) at less-than-optimal resolution. Therefore, we develop EagleC, a framework that combines deep-learning and ensemble-learning strategies to predict a full range of SVs at high resolution. We show that EagleC can uniquely capture a set of fusion genes that are missed by whole-genome sequencing or nanopore. Furthermore, EagleC also effectively captures SVs in other chromatin interaction platforms, such as HiChIP, Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), and capture Hi-C. We apply EagleC in more than 100 cancer cell lines and primary tumors and identify a valuable set of high-quality SVs. Last, we demonstrate that EagleC can be applied to single-cell Hi-C and used to study the SV heterogeneity in primary tumors.

Identifying plant genes shaping microbiota composition in the barley rhizosphere

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections.

During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures.

HGG-02. Epigenetic transcription regulation and 3D genome structure in pediatric high-grade glioma

INTRODUCTION: Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid brain tumors. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3. To investigate whether the H3K27M mutant protein is associated with distinct chromatin structure affecting transcription regulation, we generated the first high-resolution Hi-C and ATAC-Seq maps of pHGG cell lines, and integrated these with tissue and cell genomic data. METHODS: We generated sequencing data from patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1, normal brainstem n=1). Analyses included cell line RNA-Seq, ChIP-Seq (H3K27ac, H3K27me3, H3K27M) and genome-wide chromatin conformation capture (Hi-C), as well as tissue ATAC-Seq. Publicly available pediatric glioma tissue ChIP-Seq data was integrated with cell data. CRISPR knock-down of target enhancer regions was performed. RESULTS: We identified tumor-specific enhancers and regulatory networks for known oncogenes in DIPG and GBM. In DIPG, FOX, SOX, STAT and SMAD families were among top H3K27Ac enriched motifs. Significant differences in Topologically Associating Domains (TADs) and DNA looping were observed at OLIG2 and MYCN in H3K27M mutant DIPG, relative to wild-type GBM and normal cells. Pharmacologic treatment targeting H3K27Ac (BET and Bromodomain inhibition) altered these 3D structures. Functional analysis of differentially enriched enhancers in DIPG implicated SOX2, SUZ12, and TRIM24 as top activated upstream regulators. Distinct genomic structural variations leading to enhancer hijacking and gene co-amplification were identified at A2M, JAG2, and FLRT1. CONCLUSION: We show genome structural variations enhancer-promoter interactions that impact gene expression in pHGG in the presence and absence of the H3K27M mutation. Our results imply that tridimensional genome alterations may play a critical role in the pHGG epigenetic landscape and thereby contribute to pediatric gliomagenesis. Further studies examining the impact of the alterations are therefore underway.

Structural Variation in Cancer: Role, Prevalence, and Mechanisms.

Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed.

A multi-platform reference for somatic structural variation detection

Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and bioinformatic analysis pipelines. Here, we performed somatic SV analysis of the paired melanoma and normal lymphoblastoid COLO829 cell lines using four different sequencing technologies. Based on the evidence from multiple technologies combined with extensive experimental validation, we compiled a comprehensive set of carefully curated and validated somatic SVs, comprising all SV types. We demonstrate the utility of this resource by determining the SV detection performance as a function of tumor purity and sequence depth, highlighting the importance of assessing these parameters in cancer genomics projects. The truth somatic SV dataset as well as the underlying raw multi-platform sequencing data are freely available and are an important resource for community somatic benchmarking efforts.