Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Muhammad Majid,Huang Yuan

doi:10.3390/insects12090837

Abstract

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16-35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

Highlights

Eukaryotic genomes are composed of a large number of different repetitive DNA sequences [1,2,3]
The LINE, Ty3-gypsy LTR retrotransposons, and DNA repeat TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35%
In the Calliptamus italicus, Calliptamus abbreviatus, and Calliptamus barbarus genomes, the most abundant transposable elements (TEs) element was LINE, which accounted for nearly 34.7%, 33.2%, and 35.1% of the total repetitive component, respectively

Summary

Introduction

Eukaryotic genomes are composed of a large number of different repetitive DNA sequences [1,2,3]. Based on their distribution and arrangements among genomes, these are classified into two important groups: tandem repeats and interspersed repeats [4]. To describe the whole collection of different satDNA families in a genome, the term “satellitome” was proposed [6]. Other than the tandem repeats, transposable elements have been categorized into two main classes according to their mode of transposition. Class II elements are well-studied groups of repeats; their mode of transposition is “cut and paste”, requiring no RNA intermediary; they are referred to as transposons. Transposons are classified into several superfamilies according to their similarities [9,10]

Methods

Results

Conclusion