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Article

Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels

by
Keliang Lyu
1,2,
Jiajing Xiao
2,
Shiheng Lyu
1 and
Renyi Liu
2,*
1
College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2023, 24(23), 16935; https://doi.org/10.3390/ijms242316935
Submission received: 27 October 2023 / Revised: 25 November 2023 / Accepted: 27 November 2023 / Published: 29 November 2023
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)
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Abstract

:
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.

1. Introduction

Transposable elements (TEs) are mobile and repetitive DNA sequences dispersed throughout the genomes of most eukaryotes [1]. First identified in Zea mays (maize) [2], TEs make up the majority of genetic material in plant genomes [3]. For instance, TEs comprise approximately 85% of the maize genome [3]. Two classes of mobile genetic elements, RNA TEs and DNA TEs, possess the capability to replicate and relocate within the nuclear genome when they are active and even transfer horizontally across diverse species [4]. In addition, TEs can perturb host sequences and recombine homologously, causing DNA rearrangements [5], which significantly impact the genome structure and function. Recent investigations have shown that a long terminal repeat retrotransposon (LTR-RT) was inserted in the upstream of MdMYB1, resulting in the conversion of golden-skinned apples to red-skinned apples [6]. Throughout maize domestication, numerous TEs have increased alternative splicing levels in transcription factors and stress-responsive genes [7]. Furthermore, TEs exhibit remarkable rates of amplification and removal, thereby driving changes in genome size and the modification of agronomic traits [6,8,9,10]. Therefore, their significance in the realm of plant genome structure, evolution, and function is substantial.
As a crucial and abundant part of plant genomes, TEs have been used as genetic markers in plant research and breeding. Molecular marker systems based on TEs have been effectively employed in crop breeding, notably in rice and tea, enabling precise identification of desirable traits and the development of superior crops [11,12]. The use of TE-derived markers in genome-wide association studies (GWAS) may recover a large portion of single-nucleotide polymorphism (SNP)-based GWAS peaks and, in the meantime, reduce false positives associated with linkage disequilibrium among SNP markers [13]. Therefore, it is critical to carefully annotate TEs in plant genomes and perform comparative analysis of TE diversity across different species [14,15,16,17].
Strawberry belongs to the genus Fragaria of the Rosaceae family and is one of the most important fruit crops in the world. The cultivated strawberry (F. x ananassa) is an allo-octoploid species developed in Europe in the mid-18th century through hybridization between two wild octoploid ancestors (F. chiloensis and F. virginiana) [18,19,20] and contains four different subgenomes. It is widely accepted that F. vesca is a diploid ancestor that bears the closest genetic distance to the cultivated strawberry, and it became part of the octoploid strawberry genome around 1.1 million years ago [18,19,20,21]. Nonetheless, there remains substantial debate regarding the other three diploid ancestors. Edger and colleagues suggest that the other three subgenomes were provided by three different diploid ancestors, namely, F. iinumae, F. nipponica, and F. viridis [20]. However, it was also proposed that all three subgenomes were contributed solely by F. iinumae or its ancestor [22,23]. Thus, a consensus on the diploid ancestors of cultivated strawberry has not been reached, and comparative analysis of TEs in different strawberry genomes may provide a clue.
TEs are a major genetic component in strawberry genomes and may play a role in the rich phenotypic diversity of strawberry species. The Fragaria genus comprises 25 identified species that are widely distributed throughout the Northern Hemisphere [18,24,25]. Fragaria species display rich diversity in phenotypes such as disease resistance, cold tolerance, fruit color, and flavor [26,27,28], making them valuable germplasm resources for the breeding of cultivated strawberry [29,30]. In previous studies on strawberry genomes, researchers identified over 40% of TE content in each genome [20,21,25,28], but the annotation and analysis of TEs remain limited. TEs are also critical players in shaping phenotypic traits of strawberries. For example, an LTR-RT inserted into the genome of F. nilgerrensis leads to the white fruit phenotype [28,31]. In cultivated strawberry, TE-derived long non-coding RNAs (lncRNAs) are involved in strawberry growth, development, and fruit maturation through the ABA biosynthesis pathway [32]. Therefore, exploring the roles of TEs in strawberry diversity and their impact on phenotypes is an important research area.
The publication of numerous high-quality genomes of Fragaria species [20,21,22,25,28,33,34,35] provides a golden opportunity for comparative analysis of TEs in the Fragaria genomes. However, a systematic analysis of TEs in species of the Fragaria genus is still lacking. Here, we utilized ten published high-quality genomes in the Fragaria genus to construct a pan-genome TE library and performed a comprehensive identification and analysis of the TEs. The results show that TEs are an important force in shaping the strawberry genomes, and the copy numbers of different LTR-RT families reflect the genetic distance among species. Furthermore, comparison of TEs within the subgenomes of cultivated strawberry with those in their diploid ancestors suggests that F. vesca and F. iinumae, but not F. viridis, likely served as the diploid ancestors of cultivated strawberry. Therefore, this study provides new insights on the TE landscape in the strawberry genomes at different ploidy levels as well as the evolutionary history of the strawberry genomes. The TE data that we generated can also serve as an invaluable resource for investigating strawberry genome structure and evolution and for guiding strawberry breeding and phenotypic trait improvements.

2. Results

2.1. Construction of a Pan-Genome TE Library with Ten Fragaria Species

2.1.1. Pan-Genome TE Content across Genus Fragaria

Transposable elements (TEs) were identified in the genomes of ten Fragaria species at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, utilizing a de novo approach. A total of 43,648 consensus TE sequences were identified using EDTA [36], with each genome yielding between 3091 and 8001 consensus sequences (Supplementary Table S1). The F. chiloensis and F. x ananassa octoploid strawberries possess four subgenomes, leading to a higher count of TEs compared to other strawberries that have a lower ploidy level. After discarding simple repeat sequences and those less than 80 nt in length, the pan-genome TE library of strawberries was established by removing highly similar sequences from all TE sequences that were identified from each of the ten strawberry species (Figure 1). The library comprises a total of 26,226 consensus sequences (Table 1). Within this library, 7719 retrotransposons (class I) and 14,857 DNA transposons (class II) were documented (Table 1). Notably the Fragaria species exhibited a higher level of diversity among DNA transposons.
The TE annotation in the Fragaria species shows that TEs account for over 50% of the genome in every species (Figure 2 and Supplementary Table S2). Noteworthy variations in TE content were observed, with percentages ranging from 51.83% in F. viridis to 60.07% in F. nilgerrensis. Three diploid strawberries (F. mandschurica, F. viridis, F. vesca), residing in high-latitude regions and the southern Himalayas [25], exhibited lower TE content, with a rate of 52.77%, 51.83%, and 52.56%, respectively, compared to other strawberry species (55.34–60.07%), suggesting that higher latitude or lower temperature may reduce the transposition activity of TEs. On the other hand, polyploid strawberry species like F. pentaphylla and F. chiloensis had a similar TE content as that of the diploid strawberries that do not reside in high-latitude regions, ranging from 55.34% to 57.55%, suggesting polyploidization did not modify the TE content. As expected, pseudochromosome regions with a higher TE content tended to have a lower gene density (Supplementary Figures S1 and S2).

2.1.2. Diversity of TE Content in the Genome of Strawberries

Across all genomes, F. iinumae exhibited the highest proportion of LTR content (34.19%) among all TE classes (or subclasses), whereas TIR (14.33%) and Helitron (7.52%) contents were slightly lower than those in the other strawberry genomes (Figure 2 and Supplementary Table S2). In contrast to F. iinumae, the remaining strawberry genomes displayed a lower class I proportion, varying from 21.10% (F. mandschurica) to 27.46% (F. chiloensis), and a higher class II proportion, ranging from 26.37% (F. x ananassa) to 32.29% (F. nilgerrensis). In F. iinumae, the contents of various TEs superfamilies were marginally lower than those in other strawberry species, except that it had a substantially higher proportion of gypsy LTR retrotransposons (25.11%), suggesting an extensive amplification of this type of TE. The distinct TE profile of F. iinumae suggests that it has a unique TE amplification history because it was the earliest divergent diploid strawberry with a confined distribution in Japan and thus was geographically segregated from other strawberry species [25].

2.2. The Evolution History of TEs in the Fragaria Genus

2.2.1. Amplification of TE Subfamilies

Because most TEs become inactive once inserted and are subsequently subject to random mutations, the insertion time (or age) of each TE can be estimated with the Kimura 2-parameter sequence divergence between each TE and the corresponding consensus sequence. Recently inserted TEs have a lower Kimura distance, whereas old TEs have a higher Kimura distance. Therefore, graphs can be generated for different kinds of transposons, i.e., LTR and LINE retrotransposons and TIR and Helitron DNA transposons in each strawberry genome, which depict peaks of activity that mark the occurrence of transposition bursts during the evolution of strawberries (Figure 3).
The results indicate that the TE transposition activities in all strawberry genomes were generally comparable, with only minor variations. A clear recent transposition burst event was observed, with the peak located in the range of a Kimura distance level of 4–7 (Figure 3). Notably, DNA transposons predominated in strawberries, except for F. iinumae. The genome of F. iinumae was found to be predominantly composed of retrotransposons. A transposition burst of LTR retrotransposons was also observed in the genomes of two diploid strawberries, F. nilgerrensis and F. iinumae, which did not correspond to any increase in copy number of DNA transposons. Four transposition bursts with a Kimura distance greater than 10 were detected in the genome of F. vesca with a low level of TE consent. Transposition activities in the two octoploid strawberry genomes were almost identical because the two species diverged no more than 500 years ago [20,21]. A more recent transposition burst event was detected in their genomes, in addition to the major transposition burst shared by all strawberries.

2.2.2. TE Contents Are Strongly Correlated with Genome Sizes of Diploid Strawberries

Excluding the limited (only three) polyploid (tetraploid and octoploid) strawberry genomes, we tested the relationship between TE content and genome size in the remaining seven diploid strawberry genomes to examine the impact of TE content on strawberry genome size. We found a strong positive correlation between TE content and strawberry genome size (Figure 4A and Supplementary Table S2). This correlation was statistically verified by a Pearson correlation test (Pearson correlation coefficient: 0.75, p = 0.0528). The quantitative traits among species within the same phylogenetic branch are interdependent because of a shared ancestor. Therefore, we conducted phylogenetically independent contrasts (PICs) using phytools, based on a published phylogenetic tree [25,37]. After conducting PICs, we found a stronger positive correlation between TE content and diploid strawberry genome size, with a Pearson correlation coefficient of 0.85 (p = 0.0323). Therefore, transposable elements play a considerable role in determining the size of diploid strawberry genome.

2.2.3. Removal Rate of LTR-RTs and the Strawberry Genome Size

LTR retrotransposons possess two identical terminal repeats on both ends, and sequence divergence between the two LTRs can be used to estimate the insertion time for each LTR-RT. We thus calculated the insertion time for all full-length LTR-RTs in each strawberry genome and put them in insertion time bins of 500 k years (Supplementary Figure S3). Naturally, there was a declining trend in the graphs because old copies were constantly disrupted or removed from the genome (Supplementary Figure S3).
Assuming that TE sequences are removed from the genome at a constant rate, the insertion time of TE distribution can be described by an exponential function with a constant half-life rate [38]. Our calculation results suggest that LTR retrotransposons are removed or truncated from the strawberry genomes at a rate of over 2.36 Mys (million years), with a notable variation between 2.36 Mys (F. pentaphylla) and 3.74 Mys (F. nilgerrensis) (Supplementary Table S4).
We analyzed seven diploid strawberry species (Figure 4B) to investigate the relationship between LTR-RT half-life rate and genome size and found a significant positive correlation between half-life rates and genome size, supported by a Pearson correlation test (Pearson correlation coefficient: 0.85, p = 0.0334). With PIC adjustment, a stronger positive correlation was also found (Pearson correlation coefficient: 0.93, p = 7.6 × 10−3). These results suggest that a slower removal rate could lead to an increase in genome size and that LTR-RT removal plays an important role in determining the genome size of diploid strawberries.

2.2.4. The Transposition Bursts of LTR-RTs in Fragaria Genomes

The specific structure of LTR-RTs enables precise estimation of their transposition time through the genetic distance between the long terminal repeat sequences located at both ends. We computed the insertion time of intact LTR-RTs in each Fragaria genome, including 413–2103 copia elements and 155–2425 gypsy elements. A density plot of LTR-RT insertion times may reveal the transposition history of each LTR-RT family and transposition burst, especially for two main LTR-RT superfamilies, copia and gypsy (Figure 5A,B).
It is apparent that all strawberry genomes experienced a significant transposition burst in the recent past (Figure 5). The F. nilgerrensis genome appeared to have experienced two transposition bursts of copia elements, one about one million years ago and the other more than eight million years ago (Figure 5A). In comparison to other varieties of strawberries, recent copia transpositions (about 400,000 years ago) in the genomes of F. mandschurica, F. nubicola, F. pentaphylla, and F. chiloensis showed higher peak levels of burst. In both genomes of F. daltoniana and F. nilgerrensis, a gypsy transposition burst occurred approximately 4 to 5 million years ago (Figure 5B). Compared to other strawberry genomes, the gypsy transposition burst in F. mandschurica, F. nubicola, F. vesca, F. pentaphylla, and F. chiloensis occurred more recently (about 300,000 years ago) and achieved higher peak levels.

2.2.5. Recent Transposition Burst of LTR Retrotransposons

Since all strawberry genomes share a recent transposition burst of LTR-RTs within the last million years, we extracted LTR-RTs inserted during this period for further analysis. The LTR-RT copies were classified into different families using TEsorter [39], and the percentage of each LTR-RT family in the total LTR-RT copies in each species was calculated and used for clustering (Figure 6 and Supplementary Table S5). The clustering grouped F. pentaphylla, F. nubicola, F. chiloensis, and F. x ananassa, the last four species diverged from the Fragaria genus, into one cluster, whereas the others were grouped into another cluster, which is in concordance with the phylogenetic tree [20,21,25], suggesting that closely related strawberries tend to share similar LTR-RT profiles.
The higher the percentage, the more likely an LTR-RT family is one of the primary groups that was involved in recent transposition burst. Both the Ale family, a member of the copia retrotransposon, and the Athila family, a member of the gypsy retrotransposon, were found to have high copy numbers in all strawberry species, suggesting that they have had high transposition activity in the past million years. The Bianca family in the F. mandschurica, F. nubicola, and F. nubicola genomes; the Tekay family in the F. mandschurica and F. vesca genomes; and the Athila family in the F. chiloensis genome exhibited a significantly higher abundance (Figure 6). The massive number of copies of these superfamilies suggests that they were one of the primary drivers of the recent LTR-RT transposition burst in those genomes.

2.3. Evolution History of TEs in Cultivated Strawberry

2.3.1. Comparative Analysis of the TE Contribution between Cultivated Strawberry Subgenomes and Their Diploid Ancestor Genomes

The cultivated strawberry (F. x ananassa) is an allo-octoploid that originated from four diploid ancestors [19,20,33]. However, although three of these ancestors have high-quality genomes that were assembled to the chromosome level [21,22,25], only a fragmented genome assembly is available for F. nipponica [35]. Therefore, we only identified TEs in the genomes of three extant diploid ancestors: F. viridis, F. vesca, and F. iinumae. When comparing the TE content in each subgenome of F. x ananassa with that in the corresponding ancestor genome, we observed significant differences in the distribution of TE superfamilies. As evident in Figure 7B and Supplementary Tables S2 and S3, the proportion of TEs in subgenome Camarosa vesca (the subgenome that likely originated from F. vesca—please see Materials and Methods for the naming convention of the four subgenomes) was lower (50.48%) compared to that in the other three subgenomes (56.95%, 57.54%, and 57.59%, respectively). The LTR-RT content in subgenome C. vesca was notably lower than that of other subgenomes, with gypsy constituting only half of that found in other subgenomes. The class II TE copy number of subgenome C. vesca was slightly higher than that in other subgenomes.
By comparing the subgenomes and their corresponding extant diploid ancestors, differences in the landscape of TEs between cultivated strawberry and its diploid ancestors became evident (Figure 7). There were notable distinctions between the TE superfamilies of subgenome Camarosa viridis and the F. viridis genome. Aside from LTR-RTs, most elements in the C. viridis subgenome exhibited lower levels compared to the F. viridis genome. Additionally, the C. viridis subgenome had a significantly higher total TE content than that of F. viridis, with respective percentages of 57.54% and 51.83%. It is also worth noting that the content of the gypsy superfamily of LTR-RTs in subgenome C. viridis was nearly twice that of F. viridis. Similar findings were observed in subgenome C. vesca (50.48%) and the F. vesca genome (52.56%), with the exception of LTR-RTs. This difference may be attributed to TE activation during the polyploidization process of cultivated strawberry [40]. Furthermore, the proportion of all elements of subgenomes C. iinumae, C. viridis, and C. nipponica was slightly lower across TE superfamilies compared to the TE content of F. iinumae.

2.3.2. Evolution History of LTR-RTs in Cultivated Strawberry

To analyze the LTR-RT transposition history in the subgenomes of cultivated strawberry, we created a distribution curve of LTR-RT insertion times for each of the four subgenomes, as illustrated in Figure 8A,B. Our results indicate that the transposition histories of the LTR-RTs in the subgenomes of cultivated strawberry are similar. We also found a significant transposition burst of both copia and gypsy elements in the four subgenomes that occurred approximately one million years ago. Among the subgenomes, C. vesca exhibited the highest peak level. Additionally, a major transposition burst of copia that occurred further back in time was observed in the subgenomes C. iinumae and C. vesca. The subgenome C. vesca, which has a closer genetic distance to extant diploid ancestor F. vesca, showed the most significant variation. On the other hand, F. vesca displayed a more recent and higher peak level during the recent major gypsy transposition burst.
Additionally, the diversity of the LTR-RT superfamilies in the subgenomes of cultivated strawberry and their corresponding diploid ancestors over the past two million years was compared (refer to Figure 6 and Figure 7). F. vesca, the diploid ancestor with a distinct gypsy insertion time distribution compared to subgenome C. vesca [18,19,20,21], exhibited a substantially greater abundance of the Tekay family (Figure 6), suggesting that the Tekay family experienced an independent transposition burst in diploid strawberry F. vesca after the formation of cultivated strawberry.

2.3.3. Shared TEs in Cultivated Strawberry Genome and the Ancestor Genomes

It has been proposed that the cultivated strawberry (F. x ananassa) is an octoploid that originated from four diploid ancestors [19,20,33]. Although TE content in the strawberry genomes has been subject to constant changes during evolution, the TE profiles in each subgenome should have high similarity to that in the corresponding ancestor diploid genome [41,42]. To this end, we examined the shared intact LTR-RTs, TIRs, and Helitrons in the genome of cultivated strawberry and the genomes of three proposed diploid ancestors (F. nipponica was not in this analysis due to lack of a high-quality genome assembly) using the shared sequences of the pan-genome TE library. As shown in the Venn plot, the number of intact TEs shared exclusively between the genome of F. viridis and cultivated strawberry was only 165, which is significantly lower than the 431 in F. vesca and the 259 in F. iinumae (Figure 9). The low level of shared TEs between the F. viridis genome and the cultivated strawberry genome implies that F. viridis may not be a true diploid ancestor of cultivated strawberry.
We further counted the copy numbers of intact TEs shared by the subgenomes of cultivated strawberry and three proposed diploid ancestor genomes (Table 2). F. viridis and the four subgenomes shared a low copy number of intact TEs (80–120), and the highest copy number of shared TE was found between F. viridis and the subgenome C. vesca, which is the subgenome that originated from F. vesca. In contrast, the numbers of shared TE copies between the F. vesca genome and the four subgenomes of cultivated strawberry range from 127 to 516, with the highest copy number coming from the F. vesca genome and the C. vesca subgenome, which originated from F. vesca. Similarly, the numbers of shared TE copies between the F. iinumae genome and the four subgenomes of cultivated strawberry range from 73 to 243, with the highest copy number coming from the F. iinumae genome and the C. iinumae subgenome, which originated from F. iinumae. These results suggest that F. vesca and F. iinumae are true diploid ancestors of cultivated strawberry but that F. viridis may not be a true diploid ancestor.

3. Discussion

3.1. The Contributions of TE Amplification and DNA Removal to Genome Size

Transposable elements (TEs) and other repetitive sequences are crucial components of eukaryotic genomes, which are instrumental in driving changes in genome size [8,43]. The contribution of TEs to genome size is variable in different eukaryotic lineages [44]. Previous reports indicated that TEs exhibit significant species specificity [45], however, general TE databases lack specificity for the Fragaria species [46]. Here, we built a pan-genome TE library based on ten high-quality genomes in the Fragaria genus, which should serve as an important resource for TE detection and investigation in strawberry genomes. The pan-genome TE library approach can help improve the TE annotation in each genome, especially for TEs that have very low copy numbers in each genome. Comparison of TEs in multiple closely related species can give us a clear picture of TE evolution in these species, and including TE markers in genome-wide association studies may help us find the cause for certain phenotypic changes. As the number of released plant genomes continues to increase at an unprecedented speed, a pan-genome TE analysis can be applied to many other plant lineages.
This study suggests that TEs are a major force in shaping the Fragaria genomes. A strong positive correlation between TE content and genome size was observed in the Fragaria species, suggesting that the amplification efficiency of TEs is an important factor that influences the genome size. Similar results have also been reported in previous studies for rice [47], Cucurbitaceae [16], Noctuidae [48], arthropods [43], hydras [49], and vertebrates [44]. The half-life rate of TEs serves as a proxy for DNA removal, and a larger half-life rate indicates a lower rate of TE DNA removal. Our analysis of half-life of LTR-RTs suggests that the rate of DNA removal is variable in different strawberry genomes and is also a contributor to genome size. This feature is particularly evident in birds due to the extremely high rate of DNA removal caused by extreme selective pressures [50]. Further investigation of the effects of environmental conditions on strawberry genome evolution may provide additional evidence.

3.2. The Role of TEs in Strawberry Genome Evolution

TEs appear to have played a crucial role in the evolution of Fragaria genomes. F. iinumae is considered the earliest diploid strawberry diverged from other species in the Fragaria genus (approximately 7.94 million years ago) [25]. The TE composition of F. iinumae differs significantly from that of other strawberry genomes examined in our study. Its genome showed the highest content of LTR-RTs (34.19%) and the lowest content of DNA transposons (22.3%). The transposition bursts of LTR-RTs in the strawberry genomes mainly occurred in the past 2 million years, which is in line with previous findings in other Rosaceae species such as apple [51], peach [52], and plum [15]. The large number of LTR-RTs inserted in the past million years suggests that the evolution of the F. iinumae genome was primarily driven by the species-specific transposition explosions of three gypsy retrotransposon families (Athila, Ogre, and Retand). This type of genome evolution, caused by specific LTR families, has also been found in the F. vesca genome. A differential transposition burst event one million years ago was discovered between the F. vesca and the Camarosa vesca subgenomes of cultivated strawberry. In the F. vesca genome, the Tekay family, a copia retrotransposon family, has undergone massive transpositions, leading to this different transposition burst. A similar example was found in the genome of hydra [49], where the significant embedding of the CR1 family of LINE retrotransposons has resulted in genomes three times larger in brown hydras compared to green hydras. Thus, the roles of TEs in shaping plant genomes cannot be ignored.
The copy number of different LTR-RT families can serve as an indicator of the genetic divergence among Fragaria species. We utilized TEsorter to sort LTR-RTs into different families and found that the LTR-RT family composition could be used to cluster the species of the Fragaria genus into two distinct groups (Figure 6). One group comprised the species F. pentaphylla, F. nubicola, F. chiloensis, and F. x ananassa, which recently diverged from in the Fragaria lineage [20,25], whereas the other group comprised species that diverged earlier. Moreover, Fragaria species that are close in this clustering usually also have close genetic distances, suggesting that the LTR-RT family composition is a reliable indicator of genetic relationships.

3.3. New Perspective on the Diploid Ancestors of Cultivated Strawberry

This study compares the TEs present in cultivated strawberry and their potential diploid ancestors. The likelihood of a diploid species being an ancestor to the cultivated strawberry can be investigated from the TE composition perspective. The cultivated strawberry is an allo-octoploid that was derived from diploid ancestors and was originated through the hybridization of two octoploids, F. chiloensis and F. virginiana [20]. Early reports have identified F. vesca and F. iinumae as diploid ancestors [18,19]. However, there exists an open debate on the other two diploid ancestors [20,22,23,33]. The debate centers on whether F. viridis and F. nipponica are the remaining two diploid progenitors [20,22,23]. Here, we analyzed and compared the TE composition profiles of the subgenomes of cultivated strawberry and the genomes of proposed diploid ancestors. Similar TE content characteristics were discovered in F. iinumae and in three subgenomes of cultivated strawberry, including the subgenome Camarosa iinumae, the subgenome C. viridis, and the subgenome C. nipponica. Only the subgenome Camarosa vesca possessed the same TE content characteristics as F. vesca. However, F. viridis showed different TE content characteristics than all other cultivated strawberry subgenomes. Furthermore, F. vesca and F. iinumae contributed to the highest copy number of shared TEs in the corresponding subgenomes in cultivated strawberry. The contribution of F. viridis to shared TEs in cultivated strawberry was significantly lower than those from F. vesca and F. iinumae, and a similar copy number of shared TEs was distributed among four cultivated strawberry subgenomes. This fact suggests that F. vesca and F. iinumae are true ancestors of cultivated strawberry, whereas F. viridis is not. Because a chromosomal-level genome assembly is not available for F. nipponica, it was not included in our analysis, and thus, we cannot provide more evidence on whether it was a possible diploid ancestor. More extant diploid strawberry genomes need to be investigated to determine other true ancestors of the cultivated strawberry. Additionally, machine learning (ML) may be employed for accurate annotation of TEs, as it has already had a wide range of applications in genetics and genomics, such as identifying gene-splicing sites, promoters, and enhancers [53,54]. Although most TEs are non-functional by themselves, their proximity or association to functional genes may have functional consequences. Including TEs as genetic markers in machine learning models may increase the power of predictive breeding or genomic selection, which is an important method for crop improvement under diverse environments [55,56,57].

4. Materials and Methods

4.1. Genome Datasets

The genomes of ten species in the genus Fragaria, assembled at the chromosome level, were selected for the detection, annotation, and analysis of TEs. Details of the genome assembly information are provided in Supplementary Table S6. The genomes of nougou strawberry (F. iinumae) [22], huangmao strawberry (F. nilgerrensis) [28], Himalaya strawberry (F. nubicola) [33], woodland strawberry (F. vesca) [21], green strawberry (F. viridis) [25], cracked strawberry (F. daltoniana) [58], northeast strawberry (F. mandschurica) [31], five-leaf raspberry (F. pentaphylla) [25], Chilean strawberry (F. chiloensis) [34], and garden strawberry (cultivated strawberry, F. x ananassa) [20] were downloaded from the Genome Database for Rosaceae (GDR) [58]. The sequencing material used for the cultivated strawberry F. x ananassa genome was the “Camarosa” cultivar. Following the convention used by Liston and colleagues [23], the four subgenomes were referred to as Camarosa vesca, C. iinumae, C. nipponica, and C. viridis in accordance with the name of the corresponding proposed diploid progenitor, namely, F. vesca, F. iinumae F. nipponica, and F. viridis, respectively [20].

4.2. Construction of the Pan-Genome TE Library for Fragaria Species

A pan-genome TE library was constructed by combining de novo and Repbase [46] annotations for ten Fragaria species. TEs of each Fragaria species were identified using a de novo approach with EDTA (v2.1.0) [36], which uses tools such as LTR_retriever [59], TIR-Learner [60], and HelitronScanner [61] to accurately identify TEs, in addition to calling on RepeatModeler (v2.0.1) [62] to increase the sensitivity of TE identification (--sensitive 1). Subsequently, the TE sequences of each Fragaria species were merged to generate a draft TE database. Simple repeat sequences, satellite sequences, and sequences less than 80 bp in length were discarded. Redundancies in TE sequences were removed using make_panTElib.pl [63], a utility tool from EDTA [36], to obtain the Fragaria pan-genome TE library. The de-duplication parameters of make_panTElib.pl were “-miniden 80 -mincov 80”. The unknown sequences in pan-genome TE library were classified into superfamilies using DeepTE [64].

4.3. Genome Masking

The pan-genome TE library was used to mask the genomes of ten Fragaria species with EDTA [36], the “--anno 1 --step anno” was used to call on the masking software RepeatMasker (http://repeatmasker.org, accessed on 3 September 2020, version 4.1.1), and the identification step was skipped.

4.4. Kimura Distance-Based Propagation Activity Analysis

To estimate the propagation activity of transposable elements during the evolutionary history of Fragaria, we performed a Kimura-based analysis of the propagation activity of the TE subfamilies. The Kimura distance between each TE and the corresponding consensus sequence in the pan-genome TE library was calculated in alignment files using calcDivergenceFromAlign.pl, a utility tool from RepeatMasker.

4.5. Estimate the Insertion Time of LTR Retrotransposon

The insertion time of an intact LTR retrotransposon can be calculated using the genetic distance between two LTR fragments and the neutral mutation rate. The procedure was implemented as scripts in the EDTA package [36]. The Kimura distance of LTR retrotransposons was transformed into an insertion time with the equation T = K/2r, where r is the strawberry neutral mutation rate estimate, which was previously estimated to be 2.8 × 10−9 [25], and K is the Kimura 2 parameter divergence of two LTR sequences of each intact LTR retrotransposon.

4.6. Estimate the Half-Life Rate of LTR Retrotransposon

To estimate the half-life rate at which LTR retrotransposons are removed from the strawberry genome, we divided the estimated insertion times of full-length LTR retrotransposons from each genome of Fragaria into bins of 500,000 years. Assuming that LTR retrotransposons are removed from the genome at a constant rate, the distribution of insertion times can be represented by an exponential function with a constant half-life rate. To estimate the average half-life of LTR retrotransposons, an R (v4.1.1) script was used to fit an exponential function representing the relationship between insertion time and number of LTR retrotransposons to the observed data by minimizing the sum of the distance between the calculated and the observed values for each bin.

5. Conclusions

Transposable elements are an important part of the genome and play a crucial role in plant genome structure and function [5,65]. In this study, we conducted a comparative analysis of TEs in ten Fragaria genomes to enhance our understanding of the TE composition of each genome and the roles they played in strawberry genome evolution and function. The linear relationship between the half-life of intact LTR-RTs and genome size suggests that, in addition to the amplification efficiency of TEs, the rate of DNA removal is also an important force in determining strawberry genome size. The copy number of LTR-RT families over the last million years reflects the genetic distance among Fragaria species. Comparisons of TEs in the genomes of cultivated and diploid strawberries suggest that F. vesca and F. iinumae are diploid ancestors of cultivated strawberry but that F. viridis may not be. More high-quality strawberry genomes are necessary to determine additional diploid ancestors of cultivated strawberry.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms242316935/s1.

Author Contributions

Methodology and data analysis, K.L.; writing—original draft preparation, K.L.; writing—review and editing, J.X., S.L. and R.L.; visualization, K.L.; supervision, J.X. and R.L. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by funds from Fujian Agriculture and Forestry University to R.L.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained within the article.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. The pipeline for building a pan-genome TE library and annotating TEs in the Fragaria genomes.
Figure 1. The pipeline for building a pan-genome TE library and annotating TEs in the Fragaria genomes.
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Figure 2. Percentages of genome occupied by TEs in the different Fragaria genomes studied. The genome percentages of LTR (long terminal repeat) and LINE (long interspersed nuclear element) retrotransposons; TIR (terminal inverted repeat) and Helitron DNA transposons; and unclassified elements (Unknown) were estimated with EDTA. For clarity, DIRS (Dictyostelium intermediate repeat sequence) sequences were included in LTR retrotransposons, and PLE (Penelope-like element) sequences were included in LINE elements.
Figure 2. Percentages of genome occupied by TEs in the different Fragaria genomes studied. The genome percentages of LTR (long terminal repeat) and LINE (long interspersed nuclear element) retrotransposons; TIR (terminal inverted repeat) and Helitron DNA transposons; and unclassified elements (Unknown) were estimated with EDTA. For clarity, DIRS (Dictyostelium intermediate repeat sequence) sequences were included in LTR retrotransposons, and PLE (Penelope-like element) sequences were included in LINE elements.
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Figure 3. Kimura distance-based divergence analysis of TEs in Fragaria genomes. These graphs represent the genome coverage for different types of TEs (LTR and LINE retrotransposons; TIR and Helitron DNA transposons) in the analyzed genomes, clustered according to the Kimura distance of TE copies and their corresponding consensus sequences. For clarity, DIRS sequences are included in LTR retrotransposons and PLE elements in LINE elements.
Figure 3. Kimura distance-based divergence analysis of TEs in Fragaria genomes. These graphs represent the genome coverage for different types of TEs (LTR and LINE retrotransposons; TIR and Helitron DNA transposons) in the analyzed genomes, clustered according to the Kimura distance of TE copies and their corresponding consensus sequences. For clarity, DIRS sequences are included in LTR retrotransposons and PLE elements in LINE elements.
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Figure 4. (A) Correlation between genome size and content of TEs) and (B) between genome size and the half-life rate of LTR-RTs in diploid strawberry genomes.
Figure 4. (A) Correlation between genome size and content of TEs) and (B) between genome size and the half-life rate of LTR-RTs in diploid strawberry genomes.
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Figure 5. Density plot of LTR-RT insertion times in the Fragaria genomes. Colored lines represent different strawberry species. (A) Density plot of copia retrotransposon insertion time in the Fragaria genomes (dashed line at x = 0.4 Mya). (B) Density plot of gypsy retrotransposon insertion time in the Fragaria genomes (dashed line at x = 0.3 Mya).
Figure 5. Density plot of LTR-RT insertion times in the Fragaria genomes. Colored lines represent different strawberry species. (A) Density plot of copia retrotransposon insertion time in the Fragaria genomes (dashed line at x = 0.4 Mya). (B) Density plot of gypsy retrotransposon insertion time in the Fragaria genomes (dashed line at x = 0.3 Mya).
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Figure 6. Diversity and abundance of LTR retrotransposon superfamilies that have transposed within the last 1 million years. The family of LTR retrotransposons is identified by TEsorter [39]. Percentages of LTR-RT superfamilies in total LTR-RTs of Fragaria genomes are represented by different colors. Percentage values were log 2 transformed.
Figure 6. Diversity and abundance of LTR retrotransposon superfamilies that have transposed within the last 1 million years. The family of LTR retrotransposons is identified by TEsorter [39]. Percentages of LTR-RT superfamilies in total LTR-RTs of Fragaria genomes are represented by different colors. Percentage values were log 2 transformed.
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Figure 7. Percentages of TEs in extant diploid Fragaria ancestor genomes and the corresponding cultivated strawberry subgenomes. (A) Percentages of different types of TEs in the genomes of extant diploid ancestors. (B) Percentages of different types of TEs in the subgenomes of cultivated strawberry. For clarity, DIRS sequences were included in LTR retrotransposons and PLE elements were included in LINE elements.
Figure 7. Percentages of TEs in extant diploid Fragaria ancestor genomes and the corresponding cultivated strawberry subgenomes. (A) Percentages of different types of TEs in the genomes of extant diploid ancestors. (B) Percentages of different types of TEs in the subgenomes of cultivated strawberry. For clarity, DIRS sequences were included in LTR retrotransposons and PLE elements were included in LINE elements.
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Figure 8. Density plot of LTR-RT insertion times in the subgenomes of cultivated strawberry. Colored lines represent different subgenomes. (A) Density plot of copia retrotransposon insertion times in the subgenomes (dashed line at x = 1 Mya). (B) Density plot of gypsy retrotransposon insertion times in the subgenomes (dashed line at x = 1 Mya).
Figure 8. Density plot of LTR-RT insertion times in the subgenomes of cultivated strawberry. Colored lines represent different subgenomes. (A) Density plot of copia retrotransposon insertion times in the subgenomes (dashed line at x = 1 Mya). (B) Density plot of gypsy retrotransposon insertion times in the subgenomes (dashed line at x = 1 Mya).
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Figure 9. Venn diagram for intact TEs shared between cultivated strawberry and three proposed diploid ancestors.
Figure 9. Venn diagram for intact TEs shared between cultivated strawberry and three proposed diploid ancestors.
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Table 1. Summary of the pan-genome TE library of Fragaria species.
Table 1. Summary of the pan-genome TE library of Fragaria species.
Type of TENumber of Sequences
Class I 8931
LTR 8539
Copia3002
Gypsy5255
Unknown282
NonLTR 392
LINE320
SINE46
DIRS3
PLE23
Class II 16,154
TIR13,945
CACTA3928
Mutator5007
P2
PIF-Harbinger1408
Tc1-Mariner517
hAT3083
Helitron2209
Unknown 1141
Total 26,226
Table 2. Number of TEs shared by the subgenomes of cultivated strawberry and three proposed diploid ancestors.
Table 2. Number of TEs shared by the subgenomes of cultivated strawberry and three proposed diploid ancestors.
SubgenomeTotalF. viridisF. vescaF. iinumae
Camarosa viridis163985127157
Camarosa vesca213612051673
Camarosa iinumae185582139243
Camarosa nipponica182480151154
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Lyu, K.; Xiao, J.; Lyu, S.; Liu, R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int. J. Mol. Sci. 2023, 24, 16935. https://doi.org/10.3390/ijms242316935

AMA Style

Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. International Journal of Molecular Sciences. 2023; 24(23):16935. https://doi.org/10.3390/ijms242316935

Chicago/Turabian Style

Lyu, Keliang, Jiajing Xiao, Shiheng Lyu, and Renyi Liu. 2023. "Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels" International Journal of Molecular Sciences 24, no. 23: 16935. https://doi.org/10.3390/ijms242316935

APA Style

Lyu, K., Xiao, J., Lyu, S., & Liu, R. (2023). Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. International Journal of Molecular Sciences, 24(23), 16935. https://doi.org/10.3390/ijms242316935

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