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. 2019 Jun 30;514(3):726-733.
doi: 10.1016/j.bbrc.2019.04.192. Epub 2019 May 8.

Conserved microsatellites may contribute to stem-loop structures in 5', 3' terminals of Ebolavirus genomes

Douyue Li  1 , Hongxi Zhang  1 , Shan Peng  1 , Saichao Pan  1 , Zhongyang Tan  2
Affiliations

Conserved microsatellites may contribute to stem-loop structures in 5', 3' terminals of Ebolavirus genomes

Douyue Li et al. Biochem Biophys Res Commun. .

Abstract

Microsatellites (SSRs) are ubiquitous in coding and non-coding regions of the Ebolavirus genomes. We synthetically analyzed the microsatellites in whole-genome and terminal regions of 219 Ebolavirus genomes from five species. The Ebolavirus sequences were observed with small intraspecies variations and large interspecific variations, especially in the terminal non-coding regions. Only five conserved microsatellites were detected in the complete genomes, and four of them which well base-paired to help forming conserved stem-loop structures mainly appeared in the terminal non-coding regions. These results suggest that the conserved microsatellites may be evolutionary selected to form conserved secondary structures in 5', 3' terminals of Ebolavirus genomes. It may help to understand the biological significance of microsatellites in Ebolavirus and also other virus genomes.

Keywords: Conserved microsatellite; Conserved stem-loop structure; Ebolavirus; Evolutionary selection.

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Figures

Fig. 1
Fig. 1
Sequence diversity in 5′, 3′ terminal regions and complete genomes of Ebolavirus. (A)Intraspecies variations of complete genomes. (B) Intraspecies variations of 5′ terminal sequences. (C) Intraspecies variations of 3′ terminal sequences. (D) Interspecific variations of complete genomes. (E) Interspecific variations of 5′ terminal sequences. (F) Interspecific variations of 3′ terminal sequences. Species 1 and Species 2 are the distinctions between different sequences for pairwise alignment, respectively. Species 1 includes the sequences of Z1-Z184, B1—B8, R1-R9, and Species 2 includes the sequences of B1—B8, R1-R9, S1—S15.
Fig. 2
Fig. 2
High conserved microsatellites loci mainly occurred in 5′, 3′ terminal sequences. (A) Total of microsatellites in the complete genomes and 5′, 3′ terminal sequences. (B) Sequences of five conserved microsatellite loci. (C) Conserved rate of complete genomes and terminal sequences. (D) Relative abundance of complete genomes and terminal sequences. * indicates that they have the same base. Blue is used to represent conserved microsatellites, and different bases on highly conserved microsatellites are represented in red. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3
Fig. 3
Conserved microsatellites were located on conserved stem-loop structures. (A) Stem-loop structures of 5 species of Ebolavirus in the 5′ terminal sequences. (B) Stem-loop structures of 5 species of Ebolavirus in the 3′ terminal sequences. Red is used to represent conserved microsatellites, and different bases on highly conserved microsatellites are represented in blue. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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