title: Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.
abstract: DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.
authors: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;
authors: Ji
authors: J
authors: Qi
authors: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;
authors: Yamao
authors: Y
authors: Chen
authors: Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280;Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599-3280; and.
authors: Gregory P
authors: GP
authors: Copenhaver
authors: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, andMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Sciences, Fudan University, Shanghai 200433, China;Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China hongma@fudan.edu.cn.
authors: Hong
authors: H
authors: Ma
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D006801:Humans; D008540:Meiosis / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
chemical_list: D018744:DNA, Plant
keywords: genotyping; high-throughput sequencing; insertions–deletions; structural variation