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New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species.
Genes (Basel). 2019 04 09; 10(4)G

Abstract

The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.

Authors+Show Affiliations

State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China. mbzls@swu.edu.cn.State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China. miffyjolia@sina.com.State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China. mulberry201@email.swu.edu.cn.State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China. hejia@swu.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30970574

Citation

Ma, Bi, et al. "New Insights Into Long Terminal Repeat Retrotransposons in Mulberry Species." Genes, vol. 10, no. 4, 2019.
Ma B, Kuang L, Xin Y, et al. New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species. Genes (Basel). 2019;10(4).
Ma, B., Kuang, L., Xin, Y., & He, N. (2019). New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species. Genes, 10(4). https://doi.org/10.3390/genes10040285
Ma B, et al. New Insights Into Long Terminal Repeat Retrotransposons in Mulberry Species. Genes (Basel). 2019 04 9;10(4) PubMed PMID: 30970574.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species. AU - Ma,Bi, AU - Kuang,Lulu, AU - Xin,Youchao, AU - He,Ningjia, Y1 - 2019/04/09/ PY - 2019/02/22/received PY - 2019/03/27/revised PY - 2019/04/04/accepted PY - 2019/4/12/entrez PY - 2019/4/12/pubmed PY - 2019/4/12/medline KW - Copia KW - Gypsy KW - Long terminal repeat (LTR) retrotransposons KW - Morus notabilis KW - insertion time KW - transposable elements JF - Genes JO - Genes (Basel) VL - 10 IS - 4 N2 - The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome. SN - 2073-4425 UR - https://www.unboundmedicine.com/medline/citation/30970574/New_Insights_into_Long_Terminal_Repeat_Retrotransposons_in_Mulberry_Species_ L2 - http://www.mdpi.com/resolver?pii=genes10040285 DB - PRIME DP - Unbound Medicine ER -