Genome-wide analysis of LTR-retrotransposons in oil palm.

Thierry Beulé,Estelle Jaligot,Romain Guyot,Stephane Dussert,Mawussé DT Agbessi

doi:10.1186/s12864-015-2023-1

Abstract

BackgroundThe oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world’s largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences.MethodsIn this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data.ResultsOur results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome.ConclusionsConsidering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2023-1) contains supplementary material, which is available to authorized users.

Highlights

The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world’s largest source of edible vegetable oil
De novo construction and analysis of consensus Transposable Elements (TE) databases A total of 991 E. oleifera (Eo) and 846 E. guineensis (Eg) scaffolds were used for self-comparison in order to detect repeated sequences within each dataset
Among the Long terminal repeat (LTR) retrotransposons that form the major part of the TE fraction, we discovered a comparable diversity within the Gypsy and Copia super-families between both oil palm genomes

Summary

Introduction

The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world’s largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. Transposable Elements (TEs) are mobile and parasitic nucleic acids that can be distinguished according to their respective mode of transposition. TEs make up a significant fraction of many eukaryotic genomes and, in plants, the increase in TE content is Because of their replication mode, retrotransposons constitute the most abundant TE class. Among them, those with Long Terminal Repeats (LTRs), belonging to Gypsy and Copia super-families are largely predominant in the genomes of flowering plants [1, 9]. When annotating TE sequences in genomes, further distinction is between autonomous and non-autonomous elements based on the presence or the absence, respectively, of both the POL and GAG coding domains that are required for transposition, regardless of whether these sequences are functional [1, 10].

Methods

Results

Discussion

Conclusion