Abstract
Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41-81%. Class I retrotransposons covered 36-75% of these species' draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56-2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87-3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.
Highlights
Eukaryotic genomes are known to be densely populated with different types of repetitive elements, including tandem repeats [1] and transposable elements (TEs) [2]
To assess the completeness of each of the four genome assemblies, we adopted the Benchmarking Universal Single-Copy Orthologs (BUSCO) plant lineage dataset, which consists of 1440 single-copy orthologs for the Embryophyta lineage
This library of Transposable elements (TEs) candidates encompasses both Class I (LTR-reverse transcriptase (RT), non-Long terminal repeat (LTR) retrotransposons) and Class II elements (TIR elements, Helitrons, and Miniature inverted-repeat transposable element (MITE)), which are provided in Supplementary files 1–4
Summary
Eukaryotic genomes are known to be densely populated with different types of repetitive elements, including tandem repeats [1] and transposable elements (TEs) [2]. McClintock, who discovered genes that move from one chromosome to another and, in so doing, affect the phenotype of the host organism [3, 4]. Thousands or even tens of thousands of TE families exist in plants [5]. They have conquered thousands of different families in the plant kingdom [6], making up anywhere from 14% of a plant’s genome (as in Arabidopsis thaliana [7]) to over 80% Plants are the front line for investigating the impact of TEs on genome structure and gene expression. Recent insertions of TE families have proven to be helpful in better understanding the evolutionary mechanisms involved in species differentiation [10]
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