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Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
Lu, Pingli2,3; Han, Xinwei2,3,4; Qi, Ji5,6; Yang, Jiange2,3; Wijeratne, Asela J.2,3,7; Li, Tao1; Ma, Hong5,6; Li, T (reprint author), Chinese Acad Sci, Inst Hydrol, Wuhan 430072, Peoples R China
2012-03-01
Source PublicationGENOME RESEARCH
ISSN1088-9051
Volume22Issue:3Pages:508-518
AbstractMeiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 943 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enrichment for disease-resistance genes. Another 316 genes are affected by large indels, including 130 genes with complete deletion of coding regions in Ler. Using the Arabidopsis qrtl mutant, two sets of four meiotic products were generated and analyzed by sequencing for meiotic recombination, representing the first tetrad analysis with whole-genome sequencing in a nonfungal species. We detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed genome variation in meiotic products, contributing to population diversity. In particular, meiosis provides a rapid mechanism to generate copy-number variation (CNV) of sequences that have different chromosomal positions in Col and Ler.; Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 943 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enrichment for disease-resistance genes. Another 316 genes are affected by large indels, including 130 genes with complete deletion of coding regions in Ler. Using the Arabidopsis qrtl mutant, two sets of four meiotic products were generated and analyzed by sequencing for meiotic recombination, representing the first tetrad analysis with whole-genome sequencing in a nonfungal species. We detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed genome variation in meiotic products, contributing to population diversity. In particular, meiosis provides a rapid mechanism to generate copy-number variation (CNV) of sequences that have different chromosomal positions in Col and Ler.
SubtypeArticle
Department[Li, Tao] Chinese Acad Sci, Inst Hydrol, Wuhan 430072, Peoples R China; [Lu, Pingli; Han, Xinwei; Yang, Jiange; Wijeratne, Asela J.] Penn State Univ, Dept Biol, University Pk, PA 16802 USA; [Lu, Pingli; Han, Xinwei; Yang, Jiange; Wijeratne, Asela J.] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA; [Han, Xinwei] Penn State Univ, Intercoll Grad Program Genet, University Pk, PA 16802 USA; [Qi, Ji; Ma, Hong] Fudan Univ, State Key Lab Genet Engn, Inst Plant Biol, Ctr Evolutionary Biol,Sch Life Sci, Shanghai 200433, Peoples R China; [Qi, Ji; Ma, Hong] Fudan Univ, Inst Biomed Sci, Shanghai 200032, Peoples R China; [Wijeratne, Asela J.] Penn State Univ, Intercoll Grad Program Plant Biol, University Pk, PA 16802 USA
DOI10.1101/gr.127522.111
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationInstitute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000300962600010
WOS KeywordCOPY NUMBER VARIATION ; NATURAL VARIATION ; STRUCTURAL VARIATION ; MAJOR DETERMINANT ; MISMATCH REPAIR ; THALIANA ; CROSSOVERS ; SEQUENCE ; YEAST ; RESOLUTION
Funding OrganizationInstitute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University ; Institute of Hydrobiology; Biology Department; Huck Institutes of the Life Sciences at the Pennsylvania State University
Citation statistics
Cited Times:74[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16767
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorLi, T (reprint author), Chinese Acad Sci, Inst Hydrol, Wuhan 430072, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrol, Wuhan 430072, Peoples R China
2.Penn State Univ, Dept Biol, University Pk, PA 16802 USA
3.Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
4.Penn State Univ, Intercoll Grad Program Genet, University Pk, PA 16802 USA
5.Fudan Univ, State Key Lab Genet Engn, Inst Plant Biol, Ctr Evolutionary Biol,Sch Life Sci, Shanghai 200433, Peoples R China
6.Fudan Univ, Inst Biomed Sci, Shanghai 200032, Peoples R China
7.Penn State Univ, Intercoll Grad Program Plant Biol, University Pk, PA 16802 USA
Recommended Citation
GB/T 7714
Lu, Pingli,Han, Xinwei,Qi, Ji,et al. Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis[J]. GENOME RESEARCH,2012,22(3):508-518.
APA Lu, Pingli.,Han, Xinwei.,Qi, Ji.,Yang, Jiange.,Wijeratne, Asela J..,...&Li, T .(2012).Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis.GENOME RESEARCH,22(3),508-518.
MLA Lu, Pingli,et al."Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis".GENOME RESEARCH 22.3(2012):508-518.
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