PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Kofler, Robert; Orozco‐terWengel, Pablo; Maio, Nicola De; Pandey, Ram Vinay; Nolte, Viola; Futschik, Andreas; Kosiol, Carolin; Schlötterer, Christian

doi:10.1371/journal.pone.0015925

Cited by 571 publications

(704 citation statements)

References 32 publications

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“…Our yields of precipitated DNA were too low to enable estimations in 3 of the 8 line replicates (both Australian background-Australian haplotype lines, and one Canadian background-Australian haplotype line). Prior to mapping, reads were trimmed from the 3 end to remove low-quality bases using Popoolation1 v1.2.2 [63] using default settings and a quality threshold of 20. Then reads were mapped to the D. melanogaster reference genome (Release 6; http://flybase.org) using BWA v.7.12-5 [64] using default settings followed by mapping of all unmapped reads using Stampy v1.0.28 [65].…”

Section: Sequence Analysismentioning

confidence: 99%

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

et al. 2018

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Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.

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Section: Sequence Analysismentioning

confidence: 99%

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

et al. 2018

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“…Regions separated by , 500 kb were merged into a single continuous region. Nucleotide diversity (p) within each breed was calculated using an identical sliding window approach as before for F ST using the PoPoolation package (Kofler et al 2011a). …”

Section: Scan For Selective Sweepsmentioning

confidence: 99%

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

Carneiro

Archer

et al. 2017

Genetics

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The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a 12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4-29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

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“…We performed multiple alignments of the D. mauritiana, a D. simulans, the D. sechellia r.1.3, and the D. melanogaster r. 5.32 genome sequences using MAUVE (Darling et al 2010) and calculated pairwise divergence Dxy between them using the PoPoolation package (Kofler et al 2011). We used CAIcal v. 1.4 (Puigbo et al 2008) to determine the Codon Adaptation Index (CAI), originally developed by Sharp and Li (1987).…”

Section: Divergence Estimates and Codon Usage Analysismentioning

confidence: 99%

“…Minimum requirements for coverage and allele count used in SNP calling are detailed in Supplemental Methods. Analyses of p and Tajima's D were performed with the PoPoolation package (Kofler et al 2011). To test for recurrent positive selection in the D. mauritiana lineage, we performed McDonald-Kreitman tests.…”

Section: Divergence Estimates and Codon Usage Analysismentioning

confidence: 99%

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Nolte¹,

Pandey²,

Kofler³

et al. 2012

Genome Res.

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117

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Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana. Two large genomic regions (>500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana. Further evidence for strong adaptive evolution was detected for several nucleoporin genes, some of which were not previously identified as genes involved in genomic conflict. Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila.

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PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Cited by 571 publications

References 32 publications

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

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