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Updated: Aug 7, 2026

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
Comparing the whole-genome-shotgun and map-based sequences of the rice genome
Jun Yu1, Peixiang Ni, Gane Ka-Shu Wong
1Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China.
Abstract:
The rice genome has now been sequenced using whole-genome-shotgun and map-based methods. The relative merits of the two methods are the subject of debate, as they were in the human genome project. In this Opinion article, we will show that the serious discrepancies between the resultant sequences are mostly found in the large transposable elements such as copia and gypsy that populate the intergenic regions of plant genomes. Differences in published gene counts and polymorphism rates are similarly resolved by considering how transposable elements affect the sequence analysis.
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