ArticleBMC genomics2015
Genome-wide analysis of LTR-retrotransposons in oil palm.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in Submergence-Tolerant Rice Varieties.Rice (New York, N.Y.) · 2026Article
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
- Comparative Genomics and Draft Genome Assembly of the Elite Tunisian Date Palm Cultivar Deglet Nour: Insights into the Genetic Variations Linked to Fruit Ripening and Quality Traits.International journal of molecular sciences · 2025Article
- Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome.Journal of applied genetics · 2022Article
- Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress.Frontiers in plant science · 2022Review
- The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption.Horticulture research · 2022Article
- Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2021Article
- Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference inInternational journal of molecular sciences · 2020Article
- Post-transcriptional regulation of several biological processes involved in latex production inPeerJ · 2020Article
- Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis.Molecular biology reports · 2019Article
- The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages.PloS one · 2019Article
- Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.Genetica · 2017Article
- The landscape and structural diversity of LTR retrotransposons in Musa genome.Molecular genetics and genomics : MGG · 2017Article
- In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.Bioinformatics and biology insights · 2017Article
- Isolation, characterization, and marker utility of KCRE1, a transcriptionally active Ty1/copia retrotransposon from Kandelia candel.Molecular genetics and genomics : MGG · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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