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Gene. 2013 Dec 15;532(2):236-45. doi: 10.1016/j.gene.2013.09.033. Epub 2013 Sep 20.

New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.

Author information

1
The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China. Electronic address: fudhui@163.com.

Abstract

Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.

KEYWORDS:

Brassica; Helitron; LINE; LTR; MicroRNA; RC; RPA; Repetitive sequence; SINE; SSR; TE; TIRs; TSDs; Transposon; long interspersed element; long terminal repeat; miRNA; plant small RNA target analysis server; psRNATarget; replication protein A; rolling circle; short interspersed element; simple sequence repeat; target site duplications; terminal inverted repeats; transposable element

PMID:
24055723
DOI:
10.1016/j.gene.2013.09.033
[Indexed for MEDLINE]

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