Title

Transposon Fingerprinting Using Low Coverage Whole Genome Shotgun Sequencing in Cacao (Theobroma cacao L.) and Related Species

Authors

Saemundur Sveinsson, University of British Columbia
Navdeep Gill, University of British ColumbiaFollow
Nolan Kane, University of Colorado Boulder
Quentin Cronk, University of British Columbia

Document Type

Article

Publication Date

7-24-2013

Publication Title

BMC Genomics

Keywords

Theobroma cacao, Transposable elements, Next generation sequencing, Graph based clustering, Retrotransposon

ISSN

1471-2164

Volume

14

First Page

502

Abstract

Background

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. 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.

Comments

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

NSUWorks Citation

Sveinsson, Saemundur; Navdeep Gill; Nolan Kane; and Quentin Cronk. 2013. "Transposon Fingerprinting Using Low Coverage Whole Genome Shotgun Sequencing in Cacao (Theobroma cacao L.) and Related Species." BMC Genomics 14, (): 502. doi:https://doi.org/10.1186/1471-2164-14-502.

ORCID ID

orcid-logo http://orcid.org/0000-0003-3746-1866

DOI

https://doi.org/10.1186/1471-2164-14-502