LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes

doi:10.3389/fpls.2017.00402

	LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes
	Zeng, Fan-Chun 1; Zhao, You-Jie 1; Zhang, Que-Jie 2,3; Gao, Li-Zhi1,2
	2017-04-04
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	8 页码:1
摘要	The amplification and recombination of long terminal repeat (LTR) retrotransposons have proven to determine the size, organization, function, and evolution of most host genomes, especially very large plant genomes. However, the limitation of tools for an efficient discovery of structural complexity of LTR retrotransposons and the nested insertions is a great challenge to confront ever-growing amount of genomic sequences for many organisms. Here we developed a novel software, called as LTRtype, to characterize different types of structurally complex LTR retrotransposon elements as well as nested events. This system is capable of rapidly scanning large-scale genomic sequences and appropriately characterizing the five complex types of LTR retrotransposon elements. After testing on the Arabidopsis thaliana genome, we found that this program is able to properly annotate a large number of structurally complex elements as well as the nested insertions. Thus, LTRtype can be employed as an automatic and efficient tool that will help to reconstruct the evolutionary history of LTR retrotransposons and better understand the evolution of host genomes. LTRtype is publicly available at: http://www.plantkingdomgdb.com/LTRtype/index.html.
关键词	Ltrtype Ltr Retrotransposons Nested Insertions Structural Complexity Genome Evolution
DOI	10.3389/fpls.2017.00402
收录类别	SCI
语种	英语
WOS记录号	WOS:000398178100001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/51052
专题	中国西南野生生物种质资源库
作者单位	1.South China Agr Univ, Inst Genom & Bioinformat, Guangzhou, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Kunming, Peoples R China 3.Guangdong Acad Agr Sci, Agro biol Gene Res Ctr, Guangzhou, Peoples R China
推荐引用方式 GB/T 7714	Zeng, Fan-Chun,Zhao, You-Jie,Zhang, Que-Jie,et al. LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes[J]. FRONTIERS IN PLANT SCIENCE,2017,8:1.
APA	Zeng, Fan-Chun,Zhao, You-Jie,Zhang, Que-Jie,&Gao, Li-Zhi.(2017).LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.FRONTIERS IN PLANT SCIENCE,8,1.
MLA	Zeng, Fan-Chun,et al."LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes".FRONTIERS IN PLANT SCIENCE 8(2017):1.

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