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. 2014 Jul;13(4):296-307.
doi: 10.1093/bfgp/elu016. Epub 2014 Jun 6.

Structural variations in plant genomes

Rachit K Saxena, David Edwards, Rajeev K Varshney

Structural variations in plant genomes

Rachit K Saxena et al. Brief Funct Genomics. 2014 Jul.

Abstract

Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

Keywords: copy number variations (CNVs); inversions; next-generation sequencing (NGS); presence and absence variations (PAVs); structural variations (SVs); translocations.

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Figures

Figure 1:
Figure 1:
Two major NGS approaches to detect SVs are de novo assembly and re-sequencing. De novo assembly method is highly efficient to detect all types of SVs including CNVs, PAVs, inversions and translocations. Re-sequencing approaches are viable options to detect CNVs and PAVs.
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