Studying recombination with high-throughput sequencing: an educational primer for use with "fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome".
نویسندگان
چکیده
An article by Singh and colleagues in this issue of GENETICS quantifies variation in recombination rate across a small region of the Drosophila melanogaster genome, providing an opportunity for instructors of genetics to introduce or reinforce important concepts such as recombination and recombination rate variation, genome sequencing, and sequence features of the genome. Additional background information, a detailed explanation of the methods used in this study, and discussion questions are provided.
منابع مشابه
Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome.
Homologous recombination affects myriad aspects of genome evolution, from standing levels of nucleotide diversity to the efficacy of natural selection. Rates of crossing over show marked variability at all scales surveyed, including species-, population-, and individual-level differences. Even within genomes, crossovers are nonrandomly distributed in a wide diversity of taxa. Although intra- an...
متن کاملBias-Variance Tradeoffs in Recombination Rate Estimation.
In 2013, we and coauthors published a paper characterizing rates of recombination within the 2.1-megabase garnet-scalloped (g-sd) region of the Drosophila melanogaster X chromosome. To extract the signal of recombination in our high-throughput sequence data, we adopted a nonparametric smoothing procedure, reducing variance at the cost of biasing individual recombination rates. In doing so, we s...
متن کاملA Comment on Fine-Scale Heterogeneity in Crossover Rate in the garnet-scalloped Region of the Drosophila melanogaster X Chromosome.
A paper published in this Journal (Singh et al. 2013) estimated fine-scale recombination rates across the 2.1-Mb garnet-scalloped (g-sd) region of the Drosophila melanogaster X chromosome by pooling male progeny inheriting crossovers within the region in groups of 100 for DNA sequencing. In each pool, the proportion of the recombinant allele at each SNP therefore should be 0 to the left of the ...
متن کاملFine-Scale Crossover Rate Variation on the Caenorhabditis elegans X Chromosome
Meiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa, and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination...
متن کاملCrossover heterogeneity in the absence of hotspots in Caenorhabditis elegans.
Crossovers play mechanical roles in meiotic chromosome segregation, generate genetic diversity by producing new allelic combinations, and facilitate evolution by decoupling linked alleles. In almost every species studied to date, crossover distributions are dramatically nonuniform, differing among sexes and across genomes, with spatial variation in crossover rates on scales from whole chromosom...
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عنوان ژورنال:
- Genetics
دوره 194 2 شماره
صفحات -
تاریخ انتشار 2013