Results 11 - 20
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39
Cellular and Molecular Studies of Postembryonic Muscle
, 2010
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IDENTIFICATION OF GENES UNDER DIVERGENT SELECTION IN INTERFERTILE, BUT ECOLOGICALLY DIVERGENT
"... Abstract: In early stages of speciation with gene flow, divergent selection creates genomic regions with elevated levels of differentiation (outlier regions) interspersed by larger genomic regions that are homogenized by gene flow. Ecologically divergent, but interfertile oaks show such a pattern o ..."
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Abstract: In early stages of speciation with gene flow, divergent selection creates genomic regions with elevated levels of differentiation (outlier regions) interspersed by larger genomic regions that are homogenized by gene flow. Ecologically divergent, but interfertile oaks show such a pattern of genomic divergence and thus provide a system to identify outlier regions. The availability of a reference genome in oaks in the near future will allows us to anchor these outlier regions to the genome sequence and to identify genes with putative role in adaptive divergence and reproductive isolation between species. Current advances in outlier screens in oaks with specific emphasis on American red oaks (section Lobatae), and comparative outliers across oak sections are reviewed. In addition, strategies are outlined to test for associations of nucleotide variation in putative outlier loci with adaptive traits that are involved in adaptive species divergence and reproductive isolation.
Bulk Segregant Analysis Followed by High-Throughput Sequencing Reveals the Neurospora Cell Cycle Gene, ndc-1, To Be Allelic
, 2011
"... With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutatio ..."
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With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutation can be identified by a single backcross to a strain enriched in SNPs compared to a standard wild-type strain. Bulk segregant analysis simultaneously increases the likelihood of determining the precise nature of the mutation. We present here a high-density SNP map between Neurospora crassaMauriceville-1-c (FGSC2225) and OR74A (FGSC2489), the strains most typically used by Neurospora researchers to carry out mapping crosses. We further have demonstrated the utility of the Mauriceville sequence and our approach by mapping the mutation responsible for the only existing temperature-sensitive (ts) cell cycle mutation in Neurospora, nuclear division cycle-1 (ndc-1). The single T-to-C point mutation maps to the gene encoding ornithine decarboxylase (ODC), spe-1 (NCU01271), and changes a Phe to a Ser residue within a highly conserved motif next to the catalytic site of the enzyme. By growth on spermidine and complementation with a wild-type spe-1 gene, we showed that the defect in spe-1 is responsible for the ts ndc-1 mutation. Based on our results, we propose changing ndc-1 to spe-1ndc, which reflects that this mutation results in an ODC with a specific nuclear division defect. Single nucleotide polymorphism (SNP) maps between or-
© The Author(s) 2013. Published by the Genetics Society of America.
"... Current de novo whole genome sequencing approaches are often inadequate for organisms lacking substantial pre-existing genetic data. Problems with these methods are manifest as: large numbers of scaffolds that are not ordered within chromosomes or assigned to individual chromosomes, misassembly of a ..."
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Current de novo whole genome sequencing approaches are often inadequate for organisms lacking substantial pre-existing genetic data. Problems with these methods are manifest as: large numbers of scaffolds that are not ordered within chromosomes or assigned to individual chromosomes, misassembly of allelic sequences as separate loci when the individual(s) being sequenced are heterozygous, and the collapse of recently duplicated sequences into a single locus, regardless of levels of heterozygosity. Here we propose a new approach for producing de novo whole genome sequences—which we call recombinant population genome construction (RPGC)—that solves many of the problems encountered in standard genome assembly, and that can be applied in model and non-model organisms. Our approach takes advantage of next-generation sequencing technologies to simultaneously barcode and sequence a large number of individuals from a recombinant population. The sequences of all recombinants can be combined to create an initial de novo assembly, followed by the use of individual recombinant genotypes to correct assembly splitting/collapsing and to order and orient scaffolds within linkage groups. RPGC can
THE GENETIC ARCHITECTURE OF JUVENILE MIGRATION IN RAINBOW TROUT
, 2013
"... This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact epubs@purdue.edu for additional information. ..."
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This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact epubs@purdue.edu for additional information.
Report The Genetic Basis of White Tigers
"... Summary The white tiger, an elusive Bengal tiger (Panthera tigris tigris) variant with white fur and dark stripes, has fascinated humans for centuries ever since its discovery in the jungles of India ..."
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Summary The white tiger, an elusive Bengal tiger (Panthera tigris tigris) variant with white fur and dark stripes, has fascinated humans for centuries ever since its discovery in the jungles of India
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"... Results and Discussion common-garden lab environment for at least two generations confirmed that the two male forms are distinct (Figure 2A)such traits arise from different genotypic changes or sharedKauai and Oahu, with Oahu flatwings more closely resem-bling normal-wing males (Figure 2A). This was ..."
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Results and Discussion common-garden lab environment for at least two generations confirmed that the two male forms are distinct (Figure 2A)such traits arise from different genotypic changes or sharedKauai and Oahu, with Oahu flatwings more closely resem-bling normal-wing males (Figure 2A). This was confirmed in*Correspondence:
stick insect Genomic consequences of multiple speciation processes in a "Data Supplement" References Subject collections Genomic consequences of multiple speciation processes in a stick insect
"... Diverse geographical modes and mechanisms of speciation are known, and individual speciation genes have now been identified. Despite this progress, genome-wide outcomes of different evolutionary processes during speciation are less understood. Here, we integrate ecological and spatial information, ..."
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Diverse geographical modes and mechanisms of speciation are known, and individual speciation genes have now been identified. Despite this progress, genome-wide outcomes of different evolutionary processes during speciation are less understood. Here, we integrate ecological and spatial information, mating trials, transplantation data and analysis of 86 130 single nucleotide polymorphisms (SNPs) in eight populations (28 pairwise comparisons) of Timema cristinae stick insects to test the effects of different factors on genomic divergence in a system undergoing ecological speciation. We find patterns consistent with effects of numerous factors, including geographical distance, gene flow, divergence in host plant use and climate, and selection against maladaptive hybridization (i.e. reinforcement). For example, the number of highly differentiated 'outlier loci', allele-frequency clines and the overall distribution of genomic differentiation were recognizably affected by these factors. Although host use has strong effects on phenotypic divergence and reproductive isolation, its effects on genomic divergence were subtler and other factors had pronounced effects. The results demonstrate how genomic data can provide new insights into speciation and how genomic divergence can be complex, yet predictable. Future work could adopt experimental, mapping and functional approaches to directly test which genetic regions are affected by selection and determine their physical location in the genome.
Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering
"... Next generation sequencing holds great promise for applications of phylogeography, landscape genetics, and population genomics in wild populations of nonmodel species, but the robustness of inferences hinges on careful experimental design and effective bioinformatic removal of predictable artifacts ..."
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Next generation sequencing holds great promise for applications of phylogeography, landscape genetics, and population genomics in wild populations of nonmodel species, but the robustness of inferences hinges on careful experimental design and effective bioinformatic removal of predictable artifacts. Addressing this issue, we use published genomes from a tunicate, stickleback, and soybean to illustrate the potential for bioinformatic artifacts and introduce a protocol to minimize two sources of error expected from similarity-based de-novo clustering of stacked reads: the splitting of alleles into different clusters, which creates false homozygosity, and the grouping of paralogs into the same cluster, which creates false heterozygosity. We present an empirical application focused on Ciona savignyi, a tunicate with very high SNP heterozygosity (∼0.05), because high diversity challenges the computational efficiency of most existing nonmodel pipelines while also potentially exacerbating paralog artifacts. The simulated and empirical data illustrate the advantages of using higher sequence difference clustering thresholds than is typical and demonstrate the utility of our protocol for efficiently identifying an optimum threshold from data without prior knowledge of heterozygosity. The empirical Ciona savignyi data also highlight null alleles as a potentially large source of false homozygosity in restriction-based reduced representation genomic data.
959 Nematode Genomes: a semantic wiki for
, 2011
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