The Drosophila melanogaster Genetic Reference Panel
Trudy F. C. Mackay,Stephen Richards,Eric A. Stone,Antonio Barbadilla,Julien F. Ayroles,Julien F. Ayroles,Dianhui Zhu,Sònia Casillas,Yi Han,Michael M. Magwire,Julie M. Cridland,Mark F. Richardson,Robert R. H. Anholt,Maite G. Barrón,Crystal Bess,Kerstin P. Blankenburg,Mary Anna Carbone,David Castellano,Lesley S. Chaboub,Laura H Duncan,Zeke Harris,Mehwish Javaid,Joy Jayaseelan,Shalini N. Jhangiani,Katherine W. Jordan,Fremiet Lara,Faye Lawrence,Sandra L. Lee,Pablo Librado,Raquel S. Linheiro,Richard F. Lyman,Aaron J. Mackey,Mala Munidasa,Donna M. Muzny,Lynne V. Nazareth,Irene Newsham,Lora Perales,Ling-Ling Pu,Carson Qu,Miquel Ràmia,Jeffrey G. Reid,Stephanie M. Rollmann,Stephanie M. Rollmann,Julio Rozas,Nehad Saada,Lavanya Turlapati,Kim C. Worley,Yuanqing Wu,Akihiko Yamamoto,Yiming Zhu,Casey M. Bergman,Kevin R. Thornton,David Mittelman,Richard A. Gibbs +53 more
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TLDR
The Drosophila melanogaster Genetic Reference Panel is described, a community resource for analysis of population genomics and quantitative traits, which reveals reduced polymorphism in centromeric autosomal regions and the X chromosomes, evidence for positive and negative selection, and rapid evolution of the X chromosome.Abstract:
A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.read more
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Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
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Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
TL;DR: This modified RADseq approach requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours.
Journal ArticleDOI
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
TL;DR: Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project, so genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres.
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