SINE Retrotransposon variation drives Ecotypic disparity in natural populations of Coilia nasus

Dong Liu,Wenqiao Tang,Ming Zhang,Jinquan Yang,Xing Zhang,Clay Matthew Royster

doi:10.1186/s13100-019-0198-8

Abstract

BackgroundSINEs are a type of nonautonomous retrotransposon that can transpose from one site to be integrated elsewhere in an organism genome. SINE insertion can give rise to genetic variants and regulate gene expression, allowing organisms to acquire new adaptive capacity. Studies on this subject have focused on the impacts of SINEs on genes. However, ecological disparities in fish have not yet been explained by SINEs.ResultsNew SINEs were isolated from Coilia nasus, which has two ecotypes—migratory and resident—that differ in their spawning and migration behaviors. The SINEs possess two structures that resemble a tRNA gene and a LINE retrotransposon tail. Comparison of olfactory tissue transcriptomes, intact SINE transcript copies were detected in only the migratory fish at the initial retrotransposition stage. The SINE DNA copy numbers were higher in the resident type than in the migratory type, while the frequency of SINE insertion was higher in the migratory type than in the resident type. Furthermore, SINE insertions can lead to new repeats of short DNA fragments in the genome, along with target site duplications. SINEs in the resident type have undergone excision via a mechanism in which predicted cleavage sites are formed by mutations, resulting in gaps that are then filled by microsatellites via microhomology-induced replication.ConclusionsNotably, SINEs in the resident type have undergone strong natural selection, causing genomic heteroplasmy and driving ecological diversity of C. nasus. Our results reveal possible evolutionary mechanisms underlying the ecological diversity at the interface between SINE mobilization and organism defense.

Highlights

Short interspersed elements (SINEs) are a type of retrotransposon frequently found in eukaryotic genomes; these elements can expand in the genome and generate multiple copies [1, 2]
We obtained 71 validated positive clones with SINEs. These SINEs vary between 178 and 285 bp in size and contain the flanking sequences of the insertion locus, which have target site duplications (TSDs) ranging from 2 to 31 nucleotides, a majority of the TSDs range in size between 3 and 8 nucleotides (Fig. 2)
SINEs underwent strong natural selection that resulted in genomic disparity between populations Given our finding that the complete RNA transcripts of SINEs were present in the migratory type but not in the resident type, we focused on examining whether SINEs had undergone natural selection in the resident type via DNA copy number analysis of SINEs

Summary

Introduction

Short interspersed elements (SINEs) are a type of retrotransposon frequently found in eukaryotic genomes; these elements can expand in the genome and generate multiple copies [1, 2]. The mobilization of these SINEs remains ongoing and continues to drive the genomic (2020) 11:4 diversity of the species [11]. In two closely related puffer fish species, transposable elements are responsible for genome size variation, with 2% SINE content in one species and 0.2% in the other [12]. SINEs are a type of nonautonomous retrotransposon that can transpose from one site to be integrated elsewhere in an organism genome. SINE insertion can give rise to genetic variants and regulate gene expression, allowing organisms to acquire new adaptive capacity. Studies on this subject have focused on the impacts of SINEs on genes. Ecological disparities in fish have not yet been explained by SINEs

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Conclusion