Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii

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• 作者：Aung Kyaw Lwin ; Edoardo Bertolini ; Mario Enrico Pè…
• 关键词：Giant reed ; Transposable elements ; Repetitive sequences ; Genome skimming
• 刊名：Molecular Genetics and Genomics
• 出版年：2017
• 出版时间：February 2017
• 年：2017
• 卷：292
• 期：1
• 页码：157-171
• 全文大小：
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Cell Biology; Biochemistry, general; Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics;
• 出版者：Springer Berlin Heidelberg
• ISSN：1617-4623
• 卷排序：292

文摘

Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C₃ grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp. It is a promising feedstock for second-generation biofuels and biomethane production. To identify and characterize the most repetitive TEs in the genomes of A. donax and its ancestral A. plinii species, we carried out low-coverage whole genome shotgun sequencing for both species. Using a de novo repeat identification approach, 33,041 and 28,237 non-redundant repetitive sequences were identified and characterized in A. donax and A. plinii genomes, representing 37.55 and 31.68% of each genome, respectively. Comparative phylogenetic analyses, including the major TE classes identified in A. donax and A. plinii, together with rice and maize TE paralogs, were carried out to understand the evolutionary relationship of the most abundant TE classes. Highly conserved copies of RIRE1-like Ty1-Copia elements were discovered in two Arundo spp. in which they represented nearly 3% of each genomic sequence. We identified and characterized the medium/highly repetitive TEs in two unexplored polyploid genomes, thus generating useful information for the study of the genomic structure, composition, and functioning of these two non-model species. We provided a valuable resource that could be exploited in any effort aimed at sequencing and assembling these two genomes.