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Genome-wide analysis of LTR-retrotransposons in oil palm.
BMC Genomics. 2015 Oct 15; 16:795.BG

Abstract

BACKGROUND

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. 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.

METHODS

In 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.

RESULTS

Our 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.

CONCLUSIONS

Considering 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.

Authors+Show Affiliations

CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. thierry.beule@cirad.fr.CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. mawusse.agbessi@gmail.com.IRD, UMR DIADE (IRD, UM), 34394, Montpellier, France. stephane.dussert@ird.fr.CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. estelle.jaligot@cirad.fr.IRD, UMR IPME (IRD, CIRAD, UM), 34394, Montpellier, France. romain.guyot@ird.fr.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26470789

Citation

Beulé, Thierry, et al. "Genome-wide Analysis of LTR-retrotransposons in Oil Palm." BMC Genomics, vol. 16, 2015, p. 795.
Beulé T, Agbessi MD, Dussert S, et al. Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics. 2015;16:795.
Beulé, T., Agbessi, M. D., Dussert, S., Jaligot, E., & Guyot, R. (2015). Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics, 16, 795. https://doi.org/10.1186/s12864-015-2023-1
Beulé T, et al. Genome-wide Analysis of LTR-retrotransposons in Oil Palm. BMC Genomics. 2015 Oct 15;16:795. PubMed PMID: 26470789.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of LTR-retrotransposons in oil palm. AU - Beulé,Thierry, AU - Agbessi,Mawussé Dt, AU - Dussert,Stephane, AU - Jaligot,Estelle, AU - Guyot,Romain, Y1 - 2015/10/15/ PY - 2015/06/23/received PY - 2015/10/07/accepted PY - 2015/10/17/entrez PY - 2015/10/17/pubmed PY - 2016/7/2/medline SP - 795 EP - 795 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: 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. 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. METHODS: In 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. RESULTS: Our 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. CONCLUSIONS: Considering 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26470789/Genome_wide_analysis_of_LTR_retrotransposons_in_oil_palm_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2023-1 DB - PRIME DP - Unbound Medicine ER -