Abstract
BackgroundTransposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species.Results(i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome.Conclusions(i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions.
Highlights
Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size
It is important to note that this method may slightly underestimate the sequencing coverage of H. balaensis and T. grandiflorum due to sequence divergence in the ultra-conserved orthologous sequences (UCOS) among the three species
The results using UCOS are consistent with results using flow cytometry genome size estimates The UCOS data was used to standardize the TE data between samples to provide relative TE abundance data
Summary
Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. Transposable elements (TEs) are a large and dynamically evolving part of plant genomes [1,2] They occupy between 15% - 84% of plant genomes [3] and TE expansion is known to cause a significant increase in genome size in many cases [4]. The most extensively studied group of class II elements transpose by a ‘cut-and-paste’ mechanism and are classified into several super-families based on sequence similarity [9]. Cut-and-paste DNA transposons are characterized by a transposase gene and a pair of flanking terminal inverted repeats (TIRS) [7]
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