Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes.

Genome Biology and Evolution
Abhijeet ShahHolger Schielzeth

Abstract

Eukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based on low coverage whole-genome sequencing to characterize the repeatomes of six species of gomphocerine grasshoppers, an insect clade characterized by unusually large and variable genome sizes. Genome sizes of the six species ranged from 8.4 to 14.0 pg DNA per haploid genome and thus include the second largest insect genome documented so far (with the largest being another acridid grasshopper). Estimated repeat content ranged from 79% to 96% and was strongly correlated with genome size. Averaged over species, these grasshopper repeatomes comprised significant amounts of DNA transposons (24%), LINE elements (21%), helitrons (13%), LTR retrotransposons (12%), and satellite DNA (8.5%). The contribution of satellite DNA was particularly variable (ranging from <1% to 33%) as was the contribution of helitrons (ranging from 7% to 20%). The age distribution of divergence within clusters was uni...Continue Reading

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Datasets Mentioned

BETA
SRR764584
SRR764591

Methods Mentioned

BETA
whole-genome shotgun sequencing
flow cytometry
PCA

Software Mentioned

BD FACSDiva
satMiner
Dfam
Trimmomatic
BLAST
Linux shell scripts
RepeatMasker
PEAR
GAMMA
RepeatExplorer

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