Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals

Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, providing support for an additional nonindependent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole-genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14- to 150-fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation.

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Confluence of genes, environment, development, and behavior in a post Genome-Wide Association Study world

Development and Psychopathology ◽

10.1017/s0954579412000648 ◽

2012 ◽

Vol 24 (4) ◽

pp. 1195-1214 ◽

Cited By ~ 34

Author(s):

Scott I. Vrieze ◽

William G. Iacono ◽

Matt McGue

Keyword(s):

Candidate Gene ◽

Genome Wide Association Study ◽

Association Studies ◽

Genomic Structure ◽

Psychological Theory ◽

Genomic Variation ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Structural Genomic ◽

Genome Wide

AbstractThis article serves to outline a research paradigm to investigate main effects and interactions of genes, environment, and development on behavior and psychiatric illness. We provide a historical context for candidate gene studies and genome-wide association studies, including benefits, limitations, and expected payoffs. Using substance use and abuse as our driving example, we then turn to the importance of etiological psychological theory in guiding genetic, environmental, and developmental research, as well as the utility of refined phenotypic measures, such as endophenotypes, in the pursuit of etiological understanding and focused tests of genetic and environmental associations. Phenotypic measurement has received considerable attention in the history of psychology and is informed by psychometrics, whereas the environment remains relatively poorly measured and is often confounded with genetic effects (i.e., gene–environment correlation). Genetically informed designs, which are no longer limited to twin and adoption studies thanks to ever-cheaper genotyping, are required to understand environmental influences. Finally, we outline the vast amount of individual difference in structural genomic variation, most of which remains to be leveraged in genetic association tests. Although the genetic data can be massive and burdensome (tens of millions of variants per person), we argue that improved understanding of genomic structure and function will provide investigators with new tools to test specific a priori hypotheses derived from etiological psychological theory, much like current candidate gene research but with less confusion and more payoff than candidate gene research has to date.

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Genome diversity in Ukraine

GigaScience ◽

10.1093/gigascience/giaa159 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Taras K Oleksyk ◽

Walter W Wolfsberger ◽

Alexandra M Weber ◽

Khrystyna Shchubelka ◽

Olga T Oleksyk ◽

...

Keyword(s):

Sequence Data ◽

Copy Number Variations ◽

Genomic Variation ◽

High Coverage ◽

Genome Data ◽

New Information ◽

Genome Wide ◽

Public Data ◽

Genome Wide Data ◽

Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

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Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11

International Journal of Molecular Sciences ◽

10.3390/ijms22115798 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5798

Author(s):

Shoko Tokumoto ◽

Yugo Miyata ◽

Ruslan Deviatiiarov ◽

Takahiro G. Yamada ◽

Yusuke Hiki ◽

...

Keyword(s):

Cell Line ◽

Cell Lines ◽

Desiccation Tolerance ◽

Expression Profiles ◽

Insect Cell Line ◽

Gene Expression Profiles ◽

Late Embryogenesis Abundant ◽

Heat Shock Factor 1 ◽

Genome Wide ◽

A Genome

The Pv11, an insect cell line established from the midge Polypedilum vanderplanki, is capable of extreme hypometabolic desiccation tolerance, so-called anhydrobiosis. We previously discovered that heat shock factor 1 (HSF1) contributes to the acquisition of desiccation tolerance by Pv11 cells, but the mechanistic details have yet to be elucidated. Here, by analyzing the gene expression profiles of newly established HSF1-knockout and -rescue cell lines, we show that HSF1 has a genome-wide effect on gene regulation in Pv11. The HSF1-knockout cells exhibit a reduced desiccation survival rate, but this is completely restored in HSF1-rescue cells. By comparing mRNA profiles of the two cell lines, we reveal that HSF1 induces anhydrobiosis-related genes, especially genes encoding late embryogenesis abundant proteins and thioredoxins, but represses a group of genes involved in basal cellular processes, thus promoting an extreme hypometabolism state in the cell. In addition, HSF1 binding motifs are enriched in the promoters of anhydrobiosis-related genes and we demonstrate binding of HSF1 to these promoters by ChIP-qPCR. Thus, HSF1 directly regulates the transcription of anhydrobiosis-related genes and consequently plays a pivotal role in the induction of anhydrobiotic ability in Pv11 cells.

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Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽

10.1186/s12864-021-07546-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cooper J. Park ◽

Nicole A. Caimi ◽

Debbie C. Buecher ◽

Ernest W. Valdez ◽

Diana E. Northup ◽

...

Keyword(s):

New Mexico ◽

Genetic Manipulation ◽

Distinct Species ◽

Biosynthetic Gene Cluster ◽

Genomic Variation ◽

Species Variation ◽

Nucleotide Polymorphisms ◽

Peptide Synthetases ◽

Genome Wide ◽

Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

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Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

Genome Biology and Evolution ◽

10.1093/gbe/evt152 ◽

2013 ◽

Vol 5 (11) ◽

pp. 2032-2050 ◽

Cited By ~ 19

Author(s):

Shu-Ye Jiang ◽

Ali Ma ◽

Rengasamy Ramamoorthy ◽

Srinivasan Ramachandran

Keyword(s):

Salinity Stress ◽

High Salinity ◽

Genomic Variation ◽

Expression Divergence ◽

High Salinity Stress ◽

Genome Wide ◽

Rice Genotypes ◽

Genome Wide Survey

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Evaluating large spontaneous deletions in a bovine cell line selected for bovine viral diarrhea virus resistance - MDBK reads mapping to regions in genome not shared with CRIB cell line v1

10.17504/protocols.io.bvv3n68n ◽

2021 ◽

Author(s):

aspen.workman not provided ◽

mike.heaton not provided ◽

Dennis A. Webster ◽

Gregory P Harhay ◽

Tim Smith ◽

...

Keyword(s):

Cell Line ◽

Bovine Viral Diarrhea Virus ◽

Virus Entry ◽

Mdbk Cell ◽

Genomic Variation ◽

Host Factors ◽

Bovine Viral Diarrhea ◽

Diarrhea Virus ◽

Viral Diarrhea ◽

Viral Diarrhea Virus

Bovine viral diarrhea virus (BVDV) entry into bovine cells involves attachment of virions to cellular receptors, internalization, and pH-dependent fusion with endosomal membranes. The primary host receptor for BVDV is CD46; however, the complete set of host factors required for virus entry is unknown. The Madin-Darby bovine kidney (MDBK) cell line is susceptible to BVDV infection, while a derivative cell line (CRIB) is resistant at the level of virus entry. We performed complete genome sequencing of each to identify genomic variation underlying the resistant phenotype with the aim of identifying host factors essential for BVDV entry. Three large compound deletions in the BVDV-resistant CRIB cell line were identified and predicted to disrupt the function or expression of the genesPTPN12,GRID2, andRABGAP1L. However, CRISPR/Cas9 mediated knockout of these genes, individually or in combination, in the parental MDBK cell line did not impact virus entry or replication. Therefore, resistance to BVDV in the CRIB cell line is not due to the apparent spontaneous loss ofPTPN12,GRID2, orRABGAP1Lgene function. Identifying the functional cause of BVDV resistance in the CRIB cell line may require more detailed comparisons of the genomes and epigenomes.

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Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system

10.1101/734442 ◽

2019 ◽

Cited By ~ 2

Author(s):

Remi L. Gratacap ◽

Tim Regan ◽

Carola E. Dehler ◽

Samuel A.M. Martin ◽

Pierre Boudinot ◽

...

Keyword(s):

Disease Resistance ◽

Cell Line ◽

Genome Editing ◽

Target Genes ◽

High Efficiency ◽

Genetic Resistance ◽

Model Organisms ◽

Fish Cell ◽

Genome Wide ◽

Lentivirus Transduction

1AbstractGenome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative disease resistance genes in cell lines, and the use of genome-wide CRISPR screens is currently limited by a lack of available tools and techniques. In the current study, an optimised protocol using lentivirus transduction for efficient integration of constructs into the genome of a Chinook salmon (Oncorhynchus tshwaytcha) cell line (CHSE-214) was developed. As proof-of-principle, two target genes were edited with high efficiency in an EGFP-Cas9 stable CHSE cell line; specifically, the exogenous, integrated EGFP and the endogenous RIG-I locus. Finally, the effective use of antibiotic selection to enrich the successfully edited targeted population was demonstrated. The optimised lentiviral-mediated CRISPR method reported here increases possibilities for efficient genome editing in salmonid cells, in particular for future applications of genome-wide CRISPR screens for disease resistance.

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