scholarly journals Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

2020 ◽  
Vol 29 (17) ◽  
pp. 3277-3298 ◽  
Author(s):  
Julian Junker ◽  
Jessica A. Rick ◽  
Peter B. McIntyre ◽  
Ismael Kimirei ◽  
Emmanuel A. Sweke ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genomic Variation ◽  
Structural Genomic

scholarly journals Structural genomic variation leads to unexpected genetic differentiation in Lake Tanganyika’s sardines

2019 ◽  
Author(s):  
Julian Junker ◽  
Jessica A. Rick ◽  
Peter B. McIntyre ◽  
Ismael Kimirei ◽  
Emmanuel A. Sweke ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Evolutionary Biology ◽  
Lake Tanganyika ◽  
Isolation By Distance ◽  
Genomic Variation ◽  
Population Declines ◽  
Structural Genomic ◽  
Important Species ◽  
Lake Kivu

AbstractIdentifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika’s two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal unexpected differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion in L. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.

scholarly journals Analysis of genetic differentiation and genomic variation to reveal potential regions of importance during maize improvement

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Xun Wu ◽  
Yongxiang Li ◽  
Xin Li ◽  
Chunhui Li ◽  
Yunsu Shi ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genomic Variation

scholarly journals Structural genome analysis in cultivated potato taxa

2019 ◽  
Vol 133 (3) ◽  
pp. 951-966 ◽  
Author(s):  
Maria Kyriakidou ◽  
Sai Reddy Achakkagari ◽  
José Héctor Gálvez López ◽  
Xinyi Zhu ◽  
Chen Yu Tang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Sequencing Data ◽  
Structural Variations ◽  
Structural Genomic ◽  
Ploidy Levels ◽  
Cultivated Potato ◽  
Number Variation

Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

scholarly journals Structural genomic variation in ischemic stroke

Neurogenetics ◽  
2008 ◽  
Vol 9 (2) ◽  
pp. 101-108 ◽  
Author(s):  
Mar Matarin ◽  
Javier Simon-Sanchez ◽  
Hon-Chung Fung ◽  
Sonja Scholz ◽  
J. Raphael Gibbs ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Genomic Variation ◽  
Structural Genomic

scholarly journals Fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits in the California Current Ecosystem

2020 ◽  
Vol 649 ◽  
pp. 67-81
Author(s):  
EMJ Lee ◽  
KG O’Malley
Keyword(s):  
Genetic Differentiation ◽  
Genetic Relatedness ◽  
California Current ◽  
Population Connectivity ◽  
Genomic Variation ◽  
Fine Scale ◽  
Dungeness Crab ◽  
Spatial And Temporal Patterns ◽  
Cancer Magister ◽  
Late Season

Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species, and this is often exemplified in species with long larval phases. Here, we used a genotyping-by-sequencing (GBS) approach to examine fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits sampled in the California Current Ecosystem. Specifically, we compared samples collected during expected- and late-season recruitment time periods within 2 consecutive years (2017 and 2018) at 2 sites in Oregon, USA (Yaquina Bay and Coos Bay). Evidence was found for high gene flow between the expected- and late-season recruits within each year and at both sites based on 1389 neutral loci. In contrast, strong genetic differentiation was observed between these 2 groups within each year and at both sites based on variation at 2 putatively adaptive loci. Contrary to prediction, the magnitude of genetic differentiation between these 2 seasonal groups was greater in 2017 when the Pacific Decadal Oscillation was stronger, upwelling was weaker, and the spring transition was later. Spatial genetic variation was not observed within 2017 or 2018. Comparing across years, expected- and late-season groups were differentiated at putatively adaptive loci. Interestingly, strong genetic differentiation was also observed between late-season groups across years. We found no evidence for cohesive larval dispersal among recruits based on genetic relatedness estimates. Overall, our findings provide evidence for high connectivity within Dungeness crab, but suggest that selective pressures and ocean conditions influence the genetic composition of larval recruits both intra- and inter-annually.

scholarly journals Genomic characterization of a pathogenic isolate of Saccharomyces cerevisiae reveals an extensive and dynamic landscape of structural variation

2021 ◽  
Author(s):  
Lydia R. Heasley ◽  
Juan Lucas Argueso
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Structural Variation ◽  
Genome Structure ◽  
Genomic Variation ◽  
Whole Genome Sequencing Data ◽  
Structural Genomic ◽  
Pathogenic Isolate ◽  
A Genome ◽  
Long Read

The budding yeast Saccharomyces cerevisiae has been extensively characterized for many decades and is a critical resource for the study of numerous facets of eukaryotic biology. Recently, the analysis of whole genome sequencing data from over 1000 natural isolates of S. cerevisiae has provided critical insights into the evolutionary landscape of this species by revealing a population structure comprised of numerous genomically diverse lineages. These survey-level analyses have been largely devoid of structural genomic information, mainly because short read sequencing is not suitable for detailed characterization of genomic architecture. Consequently, we still lack a complete perspective of the genomic variation the exists within the species. Single molecule long read sequencing technologies, such as Oxford Nanopore and PacBio, provide sequencing-based approaches with which to rigorously define the structure of a genome, and have empowered yeast geneticists to explore this poorly described realm of eukaryotic genomics. Here, we present the comprehensive genomic structural analysis of a pathogenic isolate of S. cerevisiae, YJM311. We used long read sequence analysis to construct a haplotype-phased, telomere-to-telomere length assembly of the YJM311 diploid genome and characterized the structural variations (SVs) therein. We discovered that the genome of YJM311 contains significant intragenomic structural variation, some of which imparts notable consequences to the genomic stability and developmental biology of the strain. Collectively, we outline a new methodology for creating accurate haplotype-phased genome assemblies and highlight how such genomic analyses can define the structural architectures of S. cerevisiae isolates. It is our hope that through continued structural characterization of S. cerevisiae genomes, such as we have reported here for YJM311, we will comprehensively advance our understanding of eukaryotic genome structure-function relationships, structural diversity, and evolution.

scholarly journals Mitotic systemic genomic instability in yeast

2017 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
Aline Rodrigues-Prause ◽  
V. P. Ajith ◽  
Theodore M. Gurol ◽  
Mary J. Chapman ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Chromosomal Instability ◽  
Experimental Approach ◽  
Human Cancer ◽  
Chromosomal Rearrangements ◽  
Point Mutations ◽  
Genomic Variation ◽  
Genomic Disorder ◽  
Structural Genomic

ABSTRACTConventional models of genome evolution generally include the assumption that mutations accumulate gradually and independently over time. We characterized the occurrence of sudden spikes in the accumulation of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, suggesting the existence of a mitotic systemic genomic instability process (mitSGI). We characterized the emergence of a rough colony morphology phenotype resulting from an LOH event spanning a specific locus (ACE2/ace2-A7). Surprisingly, half of the clones analyzed also carried unselected secondary LOH tracts elsewhere in their genomes. The number of secondary LOH tracts detected was 20-fold higher than expected assuming independence between mutational events. Secondary LOH tracts were not detected in control clones without a primary selected LOH event. We then measured the rates of single and double LOH at different chromosome pairs and found that coincident LOH accumulated at rates 30-100 fold higher than expected if the two underlying single LOH events occurred independently. These results were consistent between two different strain backgrounds, and in mutant strains incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population experience systemic genomic instability episodes, resulting in multiple chromosomal rearrangements over one or few generations. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts, all of which challenge the idea of gradual accumulation of structural genomic variation. Our experimental approach provides a model to further dissect the fundamental mechanisms responsible for mitSGI.SIGNIFICANCE STATEMENTPoint mutations and alterations in chromosome structure are generally thought to accumulate gradually and independently over many generations. Here, we combined complementary genetic approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). Contrary to expectations, our results provided evidence for the occurrence of non-independent accumulation of multiple LOH events over one or a few cell generations. These results are analogous to recent reports of bursts of chromosomal instability in humans. Our experimental approach provides a framework to further dissect the fundamental mechanisms underlying systemic chromosomal instability processes, including in the human cancer and genomic disorder contexts.

scholarly journals CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

2019 ◽  
Author(s):  
Vinicius da Silva ◽  
Marcel Ramos ◽  
Martien Groenen ◽  
Richard Crooijmans ◽  
Anna Johansson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Analysis ◽  
Snp Array ◽  
Genomic Variation ◽  
Next Generation Sequencing Data ◽  
Major Type ◽  
Production Traits ◽  
Sequencing Data ◽  
Structural Genomic ◽  
Downstream Analysis

Abstract Summary Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes. Availability and implementation http://bioconductor.org/packages/CNVRanger.

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