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Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber

(2015) PLANT CELL. 27(6). p.1595-1604
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
Keywords
SYNTHASE GENE, PAIRED-END, SEQUENCING DATA, FUNCTIONAL IMPACT, POPULATION-SCALE, ARABIDOPSIS-THALIANA, FALSE DISCOVERY RATE, INDEL-ASSOCIATED MUTATION, TUBERCULATE FRUIT GENE, SATIVUS L.

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Citation

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Chicago
Zhang, Zhonghua, Linyong Mao, Huiming Chen, Fengjiao Bu, Guangcun Li, Jinjing Sun, Shuai Li, et al. 2015. “Genome-wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.” Plant Cell 27 (6): 1595–1604.
APA
Zhang, Zhonghua, Mao, L., Chen, H., Bu, F., Li, G., Sun, J., Li, S., et al. (2015). Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. PLANT CELL, 27(6), 1595–1604.
Vancouver
1.
Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, et al. Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. PLANT CELL. 2015;27(6):1595–604.
MLA
Zhang, Zhonghua, Linyong Mao, Huiming Chen, et al. “Genome-wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.” PLANT CELL 27.6 (2015): 1595–1604. Print.
@article{6929958,
  abstract     = {Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.},
  author       = {Zhang, Zhonghua and Mao, Linyong and Chen, Huiming and Bu, Fengjiao and Li, Guangcun and Sun, Jinjing and Li, Shuai and Sun, Honghe and Jiao, Chen and Blakely, Rachel and Pan, Junsong and Cai, Run and Luo, Ruibang and Van de Peer, Yves and Jacobsen, Evert and Fei, Zhangjun and Huang, Sanwen},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {SYNTHASE GENE,PAIRED-END,SEQUENCING DATA,FUNCTIONAL IMPACT,POPULATION-SCALE,ARABIDOPSIS-THALIANA,FALSE DISCOVERY RATE,INDEL-ASSOCIATED MUTATION,TUBERCULATE FRUIT GENE,SATIVUS L.},
  language     = {eng},
  number       = {6},
  pages        = {1595--1604},
  title        = {Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber},
  url          = {http://dx.doi.org/10.1105/tpc.114.135848},
  volume       = {27},
  year         = {2015},
}

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