Eukaryotic genomes are known to be densely populated with different types of repetitive elements, including tandem repeats [1] and transposable elements (TEs) [2]. TEs were first characterized in plant genomes over 65 years ago by B. 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% (as in maize [8, 9]. Plants are thus the front line for investigating the impact of TEs on genome structure and gene expression. Notably, TEs can generate genetic diversity upon which selection can act, and this can be leveraged for various purposes in plant breeding programs. Recent insertions of TE families have proven to be particularly helpful in better understanding the evolutionary mechanisms involved in species differentiation [10].

TEs are classified into two major categories based on the mechanism of transposition [11]. Both classes consist of assorted subdivisions, orders, and superfamilies, as described in [12]. Class I LTR retrotransposons (LTR-RTs) represent by far the majority of TEs harbored in plant genomes [13], primarily composed of two superfamilies, Ty1/Copia and Ty3/Gypsy [12], which are differentiated based on the order of their coding domains and evolutionary divergence [14]. Class I TEs replicate via a copy-and-paste mechanism involving an RNA intermediate, whereby TE mRNA is translated into its associated proteins, including a reverse transcriptase that converts the intermediate into DNA, which is then re-inserted into the genome to generate a new copy. Other retrotransposon lineages include long and short interspersed elements (LINEs, SINEs) and the less common Penelope elements [15]. Class II TEs, or “cut-and-paste” elements, mobilize themselves using an element-encoded transposase that mediates excision and transposition of the parent element from one position to another. Terminal inverted repeat (TIR) elements are the most common subclass of so-called cut-and-paste DNA transposons [16]. Other Class II elements common in plant genomes are Helitrons, which are generally less abundant than cut-and-paste TIR transposons and use a rolling circle form of replication [17].

TEs increase their copy number within a host genome through transposition, while the host often represses their activity through epigenetic mechanisms such as RNA and chromatin-mediated silencing [18]. Once integrated into a host genome, each element is subject to mutation and to a wide array of rearrangements including internal deletions, truncations, and nested insertions. Environmental stresses (cold, heat, UV light, pathogen attack, etc.), including tissue culture stress, can cause reactivation of a variable fraction of the TE population; such reactivation is thought to contribute to the host’s short-term response to changing environmental conditions [19, 20]. In tissue culture processes specifically, well-known triggers of LTR-retrotransposon remobilization [21] have been demonstrated in plants such as rice, tobacco, and barley [22, 23, 24]. Such investigations have confirmed that TEs can contribute to somaclonal variation and promote the emergence of altered phenotypes [25].

The major members of the palm family (Arecaceae or Palmae) are considered among the tallest domesticated trees and the longest-lived monocotyledonous species [26]. Palm trees are often used as landscape plants; they are also of considerable economic importance, widely cultivated in arid and semi-arid regions from North Africa through the Middle East and the Indus Valley. Among cultivated palms, the greatest quantity of plantation area (17 million hectares) is given over to oil palms in the genus Elaeis, producing 50 million tons of palm oil annually. This genus comprises two species, Elaeis guineensis, and Elaeisoleifera, which are responsible for about 33% of vegetable oil and 35% of edible oil produced worldwide [27]. The earliest recorded cultivation of the date palm Phoenix dactylifera occurred in 3700 BCE in the area between the Euphrates and the Nile River [28]. About 5000 date palm cultivars exist around the world [29], and they are an essential species in drought and saline-affected regions, particularly Saudi Arabia, which grows $>$10% of the world’s date palm trees (14% of date production) with a representation of nearly 340 varieties [30]. This study also analyzes other palm species, including the coconut (Cocos nucifera) and the rattan (Calamus simplicifolius), that are critical ecological and socioeconomic resources for many countries, having vital roles in food security, lumber, the ornamental market, and industrial materials [31]. Characterization of the genomic variation among Phoenix dactylifera (date palm), Cocos nucifera (coconut), Calamus simplicifolius (rattan), and Elaeis oleifera (oil palm) will provide insights into the evolutionary pattern of divergence within the palm family, at least structurally and at the level of the genome sequence. Early investigations [32] reported high similarity between coconut, oil palm, and date palm in terms of segmental duplications.

In the present work, genome-wide annotation of TEs was conducted in the aforementioned species using their publicly available genome assemblies. This process involved combining several approaches for the identification and annotation of TEs based on structural features, inherent repetitiveness (de novo), and similarity to elements within existing reference libraries (homology-based) [33]. We additionally built a TE reference database to characterize the compositions of palm genome assemblies and compare their respective TE populations. The comprehensive detection and annotation of TEs is still an open topic in the area of bioinformatics [34], and this analysis provides insights into TE annotation, especially in complex genomes like those of plants.

We generated repeat libraries for each of the four palm species with available genome sequences to investigate the abundance and characteristics of repeat-derived DNA within this family. This study also facilitates the repeat-masking of DNA and provides a first step towards constructing a comprehensive palm TE catalogue. Our analysis techniques were very conservative, which may have led to an underestimation of ancient and divergent elements; such elements may have been detected as unclassified. To ensure the reliability of our results, we employed a method incorporating both known TEs and signature-based repeat identification tools.

After merging all predicted repeats and performing validation and redundancy removal, we obtained libraries containing 3526, 3563, 4542, and 2874 consensus sequences, respectively, for P. dactylifera, C. nucifera, C. simplicifolius, and E. oleifera. We then merged them into a composite master reference library and re-annotated the four genome assemblies. Doing so revealed repetitive elements as comprising a total of 229.91 Mb (41.42%) in P. dactylifera, 1714.54 Mb (81.55%) in C. nucifera, 1314.23 Mb (67.20%) in C. simplicifolius, and 647.67 Mb (46.20%) in E. oleifera. Lastly, unclassified elements comprised a small proportion of each genome sequence, ranging from 2.27–3.39% in the four genome assemblies. A more detailed breakdown is given in Table 1. All told, the examined draft genomes were similar in terms of overall repetitive content (Fig. 2B), namely that retroelements dominated the assemblies.

A strong predominance of retroelements over DNA transposons is a common feature of plant genomes [64]. Class I elements constituted 36–75% of the annotated assemblies in the present study, with LTRs comprising 34–75%. This result was expected; the larger the plant genome, the greater the chance it contains many retroelements. For example, retroelements comprise 80–85% of barley and maize genomes with size $>$3 Gb [65, 66], but only 17% of the rice genome with size less than 1 Gb [67]. Among the LTR retrotransposons in this study, we discovered all four palm genome sequences to feature comparable diversity of the Ty3/Gypsy and Ty1/Copia families, with Ty1/Copia elements being more abundant than Ty3/Gypsy. This result is consistent with a previous study conducted by [27], which revealed Ty1/Copia elements to be more abundant than Ty3/Gypsy in the oil palm. Ty1/Copia elements were also the first elements detected in palm genomes via hybridization [68, 69]. We also shed some light on the composition of LTR elements below the superfamily level for the C. simplicifolius and C. nucifera assemblies for the first time.

In our phylogenetic investigation of Ty1/Copia elements likely to be recently active, C. simplicifolius dominated the tree with 136 sequences. Notably, although Ivana consensus sequences with full domains made up a small percentage of the assembly, they comprised a high percentage of elements on the tree, with at least two low-divergence clades suggesting recent transposition events. Similarly, C. simplicifolius also contained several low-divergence clades of SIRE elements, although these were interspersed with more divergent lineages. In C. nucifera, unlike the other assemblies, the bulk of complete consensus sequences were from the Angela group, comprising about 23% of the assembly. On the phylogenetic tree, Angela elements presented a low-divergence clade for C. nucifera specifically but otherwise do not seem to have many potentially active families based on consensus sequences, as defined by our filtering metric. Within C. nucifera, recent LTR activity has been reported as dominated by Ty1/Copia in the last 2 million years, with fewer and fewer elements showing evidence of activity when approaching the present [32]. In the P. dactylifera draft genome, we detected and classified TAR/Fourf, Orcyo/Ivana, and SIRE elements, supporting the work of Nouroz and Mukaramin [70]; we also identified four other Ty1/Copia groups. Despite these elements contributing less to the tree overall, the tree contains representatives of nearly all the Ty1/Copia groups detected in the P. dactylifera assembly, including the only two Ale consensus sequences. Both C. simplicifolius and C. nucifera represent the most complete and largest assemblies of the four palm species analyzed, thus probably contributing to their bias of complete consensus sequences analyzed on the tree.

Very few non-LTR retrotransposons have been reported in plants; such elements appear more abundant in animal genomes [12, 71]. For example, SINEs may comprise up to $>$15% of primate genomes but only account for 1% or less of plant genomes in general. In the present study, we found LINEs to make up 0.54–2.30% of total repetitive elements and SINEs to be only negligibly observed, representing 0.1–0.7% of each assembly, which is in line with previous reports [30, 72]. Mao et al. [73] suggested that the forces underlying rapid changes of plant genomes may be responsible, at least in part, for the removal of old SINEs from the host genome.

We also found other classes of repetitive elements, such as Class II TEs, to be poorly represented in palm genome sequences, collectively making up 1.87–3.37% of the four annotated assemblies. The most prevalent DNA transposon super-families were the hAT, Mutator, and Helitron elements, likewise being the most abundant in previous studies [74]. In particular, members of the hAT superfamily are found in many monocots, such as the Ac-Ds family in maize [75]. Unlike other DNA transposons, Helitrons are challenging to identify because they require structural-based detection methods rather than homology. In the publication detailing HelitronScanner [46], Xiong et al. reanalyzed the genome sequences of 26 plant species and reported Helitron abundance to cover at most 2–6%, the highest percentage being in maize. In the present study, we observed Helitrons to comprise about 0.73–2.47% of each assembly, with the highest coverage being found in C. nucifera (2.47%) followed by the C. simplicifolius (2.12%) and the lowest percentage reported in P. dactylifera (0.73%).

The findings of this study will provide a valuable resource for further research into palm biology and genomics. While the investigated genome sequences were similar in terms of the content and distribution of the identified repetitive elements, differences were also observed that might be associated with factors such as different evolutionary origins or discrepancies in the assembly stages of these draft genomes. Additional research into repetitive elements in palm genome sequences, perhaps with more complete genome assemblies, would provide more information on and awareness of the genomic features of these economically important plants. Furthermore, the causes and consequences of the high degree of inter-genome variability in the distribution, amount, and relative proportion of TEs are still not wholly understood; it is essential to continue characterizing this critical fraction of eukaryotic genomes. Such characterizations can bring to light evolutionary phenomena, including genomic rearrangements and other dynamic events, that have occurred in the past and may also be underway in contemporary times.

MMM and FHA conceived and designed the experiments; MAI, TAE, BMA, SNA, MSA and MMM carried out the experiments; MAI, SNA, TAE, BMA, FHA and MMM analyzed the data; MAI, SNA, TAE, and MMM wrote the manuscript. All authors reviewed the manuscript.

Not applicable.

The authors would like to thank Guilherme Dias at the Department of Genetics and Institute of Bioinformatics, University of Georgia, for his valuable comments and suggestions to improve the quality of the manuscript. The authors would also thank Amer S. Alharthi at the General Directorate for Funds and Grants (GDFG), King Abdulaziz City for Science and Technology, for his technical support.

This study was supported by the National Centre for Biotechnology, Life Science and Environment Research Institute (Grant 37-1271), King Abdulaziz City for Science and Technology, Saudi Arabia.

The authors declare no conflict of interest.

All data generated or analysed during this study are included in this published article (and its supplementary information files).