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      Opportunities and Challenges for Genomic Data Analyses in Biobanks: A Call for Papers

      The GSA Journals are calling for submissions of papers on biobank-scale genomic data analyses. The closing date for submissions is May 31 2024.

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      The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster

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      * , 1 , * ,
      G3: Genes|Genomes|Genetics
      Genetics Society of America
      Drosophila, inversion polymorphism, eQTLs, DGRP, DPGP

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          Abstract

          Chromosomal inversions are a ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel (DGRP) to explore the effects of two cosmopolitan inversions, In( 2L) t and In( 3R) Mo, on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion-affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In( 3R) Mo but do not have SNPs in linkage disequilibrium (LD) with the inversion. We speculate that this upregulation is driven by genetic variation in mod( mdg4) that is in LD with In( 3R) Mo. We find that there is little evidence for a regional or position effect of inversions on gene expression at the chromosomal level, but do find evidence for the distal breakpoint of In( 3R) Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements.

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          Most cited references61

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          Chromosome inversions, local adaptation and speciation.

          We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests.
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            Chi-Square Tests for Goodness of Fit and Contingency Tables

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              Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

              The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia , and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                14 September 2017
                November 2017
                : 7
                : 11
                : 3659-3668
                Affiliations
                [* ]Department of Genetics, Rutgers University, Piscataway, New Jersey 08901
                []Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08901
                Author notes
                [1 ]Corresponding author: Rutgers University, SEBS-Eco, Evol and Natrl. Resources, 59 Dudley Rd., Rm. 316, New Brunswick, NJ 08901-8520. E-mail: erik.lavington@ 123456rutgers.edu
                Author information
                http://orcid.org/0000-0003-1933-9023
                http://orcid.org/0000-0003-4381-4680
                Article
                GGG_1133
                10.1534/g3.117.1133
                5677173
                28916647
                92aec2fc-d950-4b19-98e6-3bb5969e56ef
                Copyright © 2017 Lavington and Kern

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 24 July 2017
                : 05 September 2017
                Page count
                Figures: 5, Tables: 6, Equations: 1, References: 75, Pages: 10
                Categories
                Investigations

                Genetics
                drosophila,inversion polymorphism,eqtls,dgrp,dpgp
                Genetics
                drosophila, inversion polymorphism, eqtls, dgrp, dpgp

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