Open AccessDistribution and Characteristics of Transposable Elements in the Mulberry Genome
Author(s) -
Ma Bi,
Xin Youchao,
Kuang Lulu,
He Ningjia
Publication year - 2019
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2018.12.0094
Subject(s) - biology , genome , transposable element , gene , genome evolution , genome size , genetics , domestication , alternative splicing , evolutionary biology , exon
Mulberry ( Morus notabilis C. K. Schneid) leaves have been used as the food for the domesticated silkworm, Bombyx mori , for more than 5000 yr, and the mulberry–silkworm relationship is one of the best‐known and oldest models of plant defense–insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE‐rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The Copia elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE‐containing genes assigned to pathways were assigned to metabolism‐related pathways. The TE‐related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.