Title |
Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes
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Published in |
BMC Genomics, January 2013
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DOI | 10.1186/1471-2164-14-71 |
Pubmed ID | |
Authors |
Yujun Han, Shanshan Qin, Susan R Wessler |
Abstract |
Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a novel comparative analysis of class 2 TEs. To ensure consistent comparative analyses, we re-annotated class 2 TEs in Brachypodium distachyon, Oryza sativa (rice), Sorghum bicolor and Zea mays and assigned them to one of the five cut-and-paste superfamilies found in plant genomes (Tc1/mariner, PIF/Harbinger, hAT, Mutator, CACTA). We have focused on noncoding elements because of their abundance, and compared superfamily copy number, size and genomic distribution as well as correlation with the level of nearby gene expression. |
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