Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

doi:10.21203/rs.3.rs-1270987/v1

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Research Article

Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

https://doi.org/10.21203/rs.3.rs-1270987/v1

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Background

Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants.

Results

To identify active LTR-RTs in rice (Oryza sativa), we characterized 1,783 intact LTR-RTs in the rice reference genome. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, we amplified LTRs of eclDNA (ALE)-seq to uncover the current transpositional potential of the LTR-RTs in callus of the Korean rice variety Dongjin. Tos17 was discovered in callus of the reference rice variety Nipponbare, and we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in Dongjin callus. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs.

Conclusions

We identified two active LTR-RTs in the callus of Korean rice variety Dongjin using ALE-seq. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.

Long terminal repeat retrotransposon

Transposition

ALE-seq

Oryza sativa

Dongjin

Transposable elements (TEs) are mobile DNA sequences that contribute to the size variation and evolution of all eukaryotic genomes, especially plant genomes. Most plant species have a wide range of TEs, which make up more than 85% of the genome in plants with large genomes such as wheat (Triticum aestivum) and barley (Hordeum vulgare) (1-4). TEs increase their copy numbers and insert into new regions of the genome. The transposition of TEs can induce structural rearrangements, generating mutations and affecting genome stability. In addition, these movements affect gene expression and function, ultimately influencing evolution and genome adaptation (5).

TEs are divided into two classes: retrotransposons (class I), which mobilize via a copy-and-paste mechanism; and DNA transposons (class II), which transpose via a cut-and-paste mechanism (6). Long terminal repeat retrotransposons (LTR-RTs) are ubiquitous class I retrotransposons that are interspersed in all eukaryote genomes (7). In most plants, LTR-RTs contribute to genome size expansion via their rapid proliferation (8, 9). For example, LTR-RTs account for more than 70% of the maize (Zea mays) and wheat (Triticum aestivum) genomes (8, 10). Intact LTR-RTs contain two similar or identical LTRs that flank an internal region containing a functional domain, target site duplications (TSDs), a polypurine tract (PPT), and a primer-binding site (PBS) (6). Most LTR-RTs are classified into two superfamilies, Copia and Gypsy, which differ in their sequences and the composition of the internal conserved domains (6, 11). The Gypsy superfamily is the most highly represented superfamily in most plant genomes (12-14).

Since transposition of LTR-RTs is a major driving force for genome evolution, various studies have aimed to identify active LTR-RTs (15-18). The transposition cycle of LTR-RTs begins with the transcription of genomic copies, followed by reverse transcription of the LTR-RT transcripts to form cDNA, also known as extrachromosomal linear DNA (eclDNA). These eclDNAs integrate into the nucleus and influence strand transfer (19). The transpositional potential of LTR-RTs has been revealed by identifying eclDNA via amplification of LTRs of eclDNAs followed by sequencing (ALE-seq) (15).

Rice (Oryza sativa) is an important cereal crop, providing a major source of food worldwide (20). Forty percent of the rice genome consists of most known types of TEs, including LTR-RTs and DNA transposons (21). Among these, LTR-RTs make up ~22% of the rice genome (22). ALE-seq analysis was successfully used to detect eclDNAs, such as heat stress–activated Go-on and activated Tos17, in O. sativa ssp. japonica cv. Nipponbare callus (15). Although active LTR-RTs have been identified in this model rice variety, little is known about active transposition in non-reference rice varieties. Therefore, in this study, we conducted ALE-seq analysis to identify the transpositional activity during callus culture in the non-reference Korean rice variety Dongjin. To identify active LTR-RTs, we searched for structurally intact LTR-RTs in the rice genome. We identified two new active Oryco LTR-RTs showing active transpositional activity in Dongjin callus. Our findings shed light on the retrotransposition mechanism.

Identification and characterization of LTR-RTs

De novo annotation of LTR-RTs in the rice reference genome (MSU7.0; http://rice.plantbiology.msu.edu) was performed with LTRharvest using the following options: minlenltr = 100, maxlenltr = 5000, and similar = 80. The plant-specific tRNAs used to screen PBS regions were obtained from plantRNA (http://seve.ibmp.unistra.fr/plantrna/). To filter out strictly intact LTR-RTs, we also scanned for the presence of tRNA and internal domains using LTRdigest with the following options: pptlen = c(8,40), pbsalilen = c(8,40), and pbsoffset = c(0,10). The flanking 5-bp regions at the start and end of each LTR-RT with more than 60% sequence homology were considered to be TSDs. Conserved domains (such as gag and pol proteins) were investigated using the TEsorter tool, which uses the gydb database containing GAG, AP, INT, RT, and RNaseH domain sequences (41) (Additional file 2: Fig S9).

To confirm the relatedness of the annotated LTR-RT families, RT amino acid sequences for each family were aligned using MAFFT (42). The phylogenetic tree was constructed using the aligned RT amino acid sequences based on the maximum-likelihood method via IQ-TREE (43).

The pair of LTR sequences was aligned with MAFFT, and sequence divergence (k) between the pair of LTRs was estimated using Kimura’s two-parameter model (44). The insertion ages of the LTR-RTs were estimated using the formula T = k/2r (r: substitution rate of 1.3 × 10^-⁸ substitutions per site per year) (45).

Plant materials and ALE-seq analysis

Rice callus was generated from mature embryos of O. sativa ssp. japonica cv. Dongjin seeds. Dehulled seeds were sterilized with 2% sodium hypochlorite for 30 min and washed three times in sterile water. The sterilized seeds were inoculated on N6D medium containing 2 mg/L 2,4-D and cultured under continuous light at 30°C for 2 weeks (46).

Total genomic DNA was extracted from the callus using a GeneAll Plant SV Midi Kit (GeneAll Biotechnology Co. Ltd., Seoul, Korea) following the manufacturer’s protocol. Genomic DNA (300 ng) was used to generate the ALE-seq library. The first step in ALE-seq was to connect an adapter containing the T7 promoter sequence to the end of 5' end of the eclDNA, followed by in vitro transcription using T7 RNA polymerase. Reverse transcription was then performed using a primer that binds to the transcript of the PBS region, and LTR-RTs showing transposition were extracted (15). The ALE-seq library was analyzed on the Illumina MiSeq platform with 30-bp paired-end reads by Macrogen (Seoul, Korea). The raw ALE-seq data for O. sativa ssp. japonica cv. Dongjin were deposited in the National Center for Biotechnological Information (NCBI) Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/sra) (accession number: SRR17128798).

The adapter sequences and poor-quality reads were filtered from the raw reads using Trimmomatic-0.33 (47). Paired-end sequences were mapped to the rice reference genome (MSU7.0) using Bowtie2 (-X 3,000) (48). The number of reads mapped throughout each LTR-RT was counted with the FeatureCounts tool using the customized annotation file generated by de novo LTR-RT prediction pipelines (49). The IGV genome browser was used to visualize the read depth pattern (50).

Validation of active LTR-RTs in Dongjin rice

The hit positions were manually inspected to identify the complete structures of active LTR-RTs. PCR verification was conducted to confirm that the active LTR-RTs in Dongjin were present at the same location in the Dongjin genome as in the reference genome. PCR primer pairs were designed using Primer 3 (http://bioinfo.ut.ee/primer3-0.4.0/). Forward primers were located in the flanking region of LTR-RTs, whereas reverse primers were located in the internal parts of LTR-RTs. The PCR products were separated on 1% agarose gels.

BLAST searches were conducted for the putatively active LTR-RTs to examine their transcriptional activity in various tissues or cultivars. BLASTN analysis was performed using the two candidate LTR-RTs as queries against the expressed sequence tag (EST) database using the parameter settings E-value < e^–5 and identity >95%.

Identification and annotation of intact LTR-RTs

We tried to detect extrachromosomal linear DNA (eclDNA) forms of active LTR-RTs in Korean rice cultivar Dongjin by ALE-seq. The active form of an LTR-RT should contain an intact structure, including two complete LTRs, a PBS, a PPT, a TSD, and conserved internal domains. We identified 1,783 intact LTR-RTs, including 1,226 Gypsy-type (68.8%) and 557 Copia-type (31.2%) LTR-RTs, in the O. sativa reference genome sequence (Additional file 1: Table S1-3).

Phylogenetic analysis of the LTR-RTs based on their reverse transcriptase (RT) domain distinguished the Copia and Gypsy superfamilies. The Copia superfamily was grouped into the Oryco, Tork, Retrofit, and Sire families; the Gypsy superfamily was grouped into the Tat, Del, Reina, and Crm families (Additional file 2: Fig S1). The Tat family accounted for the largest number of Gypsy superfamily members and had more variants than the other families. We plotted the pattern of full-length LTR-RTs on the phylogenetic tree to examine the length distribution of the LTR-RTs across the entire family. A comparison of the LTRs on the left versus the right side for each element revealed that most elements were active during the past one million years (Myr), except for the Sire family (Additional file 1: Table S4, Additional file 2: Fig S3).

Identification of active LTR-RTs in Dongjin callus

The ALE-seq method was recently developed to identify active LTR-RTs that have retrotranspositional activity and thus produce eclDNAs. Two LTR-RTs, Tos17 and Tos19, which are known to be active in rice, were successfully detected as active LTR-RTs by ALE-seq using O. sativa cultivar Nipponbare callus (15). In this study, we conducted ALE-seq to identify active LTR-RTs in callus of another rice variety, Dongjin. Mapping of ALE-seq reads from Dongjin callus identified two active LTR-RTs located on chromosomes 6 and 9 (Figure 1). These active LTR-RTs belong to the Oryco family and were therefore named DongjinOryco1 and DongjinOryco2 (Figure 2, Additional file 1: Table S2, Additional file 2: Fig S4).

BLAST searches revealed that DongjinOryco1 and DongjinOryco2 are transcribed in various tissues, such as shoots, roots, and flowers, in diverse rice accessions (Additional file 1: Table S5-6). However, DongjinOryco1 and DongjinOryco2 were not detected in the callus of Nipponbare rice using ALE-seq. The ALE-seq reads were uniquely mapped to 5′ LTR regions and primer binding sites of the internal domains of the active LTR-RTs DongjinOryco1 and DongjinOryco2 in Dongjin callus (Figure 3a, 3b) and Tos17 in Nipponbare callus (Figure 3c), respectively. The other six Tat family members showed moderate transpositional activity, and their map positions were identified on chromosomes 1, 2, 4, 6, 8, and 12 (Additional file 1: Table S2).

Structural characteristics of DongjinOryco1 and DongjinOryco2

The active Oryco elements DongjinOryco1 and DongjinOryco2 have intact structures, including 100% identical sequences between the left and right LTR structures (Additional file 2: Fig S5) and the conserved internal domain region (GAG, AP, INT, RT, and RNaseH) (Additional file 2: Fig S6). The Oryco elements share 97% identical conserved internal sequences. However, the LTR sequences show diversity between DongjinOryco1 and DongjinOryco2, with 61% and 92% sequence similarity for the 5′ and 3′ regions of the LTRs, respectively (Figure 2, Additional file 2: Fig S4). Six other Tat family members showed relatively high (moderate) ALE-seq read depth, although the depth was much lower than that of the two Oryco family members. The Tat family members shared 59–96% sequence similarity for the entire internal region and 97.73–100% sequence similarity between the left and right LTR pair of each element (Additional file 1: Table S7, Additional file 2: Fig S6-8).

We annotated and identified the intact LTR-RTs using the Nipponbare reference genome. Since the positions of LTR-RTs can differ among varieties, we validated the chromosomal positions of DongjinOryco1 and DongjinOryco2 by PCR amplification using primers designed based on the flanking site and internal LTR-RTs located on chromosomes 6 and 9 (Figure 4).

Retrotranspositional activity and structural integrity of the active LTR-RTs

ALE-seq analysis revealed eight active LTR-RTs in Dongjin callus, which showed conserved structures, including two highly active Oryco family members and six moderately active Tat family members. The putative transposition time and retrotranscriptional activity of an LTR-RT can be estimated by comparing its LTR sequences (23) and the conservation of its internal domain regions (24). The two Oryco family members were more conserved than the six Tat family members in terms of their overall structure, suggesting that the two Oryco LTR-RTs transposed recently and maintain higher transpositional activity than the six Tat family members.

Gypsy elements are more abundant in rice than Copia elements, which is similar to findings for Solanum, Populus, and Capsicum species (12-14). Copia elements are usually more transcriptionally active than Gypsy elements. Elements that are abundant throughout the genome are more likely to be silenced by the host genome, whereas elements that are less abundant in the genome reduce the efficiency of the host’s silencing mechanisms (25-27). Tat elements belonging to the Gypsy superfamily and Oryco elements belonging to the Copia superfamily accounted for 28.49% and 4.77% of the rice LTR-RTs, respectively (Additional file 1: Table S1). Therefore, the strong retrotranspositional activity of the Oryco elements belonging to the Copia superfamily appears to be supported by their strong structural integrity as well as their lower copy numbers in the rice genome [15].

ALE-seq identifies new active LTR-RTs in Dongjin callus

LTR-RTs are transcriptionally activated when plants are exposed to environmental stress, such as heat, cold, salt, or tissue culture conditions (15, 18, 28-31). However, it is difficult to directly confirm the transpositional potential of an LTR-RT due to post-transcriptional control (32). The ALE-seq method was recently introduced to identify the direct retrotransposition potential of an LTR-RT by detection of eclDNA. Using this method, Tos17, which is known to be a major factor in tissue culture–induced mutations, was detected as having transpositional activity in the callus of O. sativa variety Nipponbare (15). The Tos17 system has greatly contributed to functional genomics studies of rice. However, this technique has been limited to Nipponbare, which was selected as a reference cultivar among japonica rice accessions (33). Because functional genomics tools are also needed for non-reference varieties, we performed ALE-seq analysis using the callus of Korean rice variety Dongjin.

Notably, Tos17 was highly active in Nipponbare callus but not in Dongjin callus (Fig. 3). Tos17 elements are activated in most rice varieties, but not in the Moritawase variety, which has higher DNA methylation levels than other varieties, although the Tos17 sequence in Moritawase is identical to that of Nipponbare. Epigenetic variation might induce the silencing of Tos17 in the Moritawase variety (34). Similarly, the Oryco family members showed high transpositional activity in Dongjin callus but not in Nipponbare callus, which may have been influenced by the various epigenetic or genetic mutations that exist between the Dongjin and Nipponbare varieties.

TE amplification generates abundant genetic diversity in domesticated cultivars of rice and many other crops (1, 35-39). The Dongjin and Nipponbare varieties exhibit large genetic variations (40). Here, we identified two active LTR-RTs, DongjinOryco1 and DongjinOryco2, in Dongjin callus but not in Nipponbare. These results suggest that the differential activation of diverse LTR-RTs might have influenced the diversification of rice varieties, a concept that requires further study.

ALE-seq is an efficient tool for identifying the active LTR-RTs that show the eclDNA structure in diverse environments and genotypes. We discovered two active Oryco LTR-RTs with retrotranspositional activity in callus culture of the rice variety Dongjin via ALE-seq. We detected variation in transpositional activity among varieties, suggesting that differences in the activities of LTR-RTs might play a role in the diversification of plant varieties. Further studies are needed to uncover the diversity of these two active Oryco elements and their roles in rice evolution and domestication.

TE: transposable element

LTR-RT: long terminal repeat retrotransposon

eclDNA: extrachromosomal linear DNA

ALE-seq: amplification of LTRs of eclDNAs followed by sequencing

EST: expressed sequence tag

Availability of data and materials

Raw read ALE-seq data are publicly available in the NCBI sequence read archive under accession number SRR17128798.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Funding

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2021R1A4A1032888).

Authors’ contributions

Conceptualization: HK and T-JY; Data analysis: HK; Validation: HK; Resources: S-JL; Writing-original draft: HK, JC and T-JY; Supervision: N-CP, JC and T-JY. All authors read and approved the final manuscript.

Acknowledgments

We appreciate Dr. Jee Young Park for assistance of research funding and management.

1. Chénais B, Caruso A, Hiard S, Casse NJG. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. 2012;509(1):7-15.

2. Jedlicka P, Lexa M, Vanat I, Hobza R, Kejnovsky EJMD. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. 2019;10(1):1-14.

3. Lanciano S, Cristofari GJNRG. Measuring and interpreting transposable element expression. 2020;21(12):721-36.

4. Zhang Q-J, Gao L-ZJGG, Genomes, Genetics. Rapid and recent evolution of LTR retrotransposons drives rice genome evolution during the speciation of AA-genome Oryza species. 2017;7(6):1875-85.

5. Shahid S, Slotkin RKJCoipb. The current revolution in transposable element biology enabled by long reads. 2020;54:49-56.

6. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. 2007;8(12):973-82.

7. Gao L, McCarthy EM, Ganko EW, McDonald JFJBG. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. 2004;5(1):1-18.

8. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. 2009;326(5956):1112-5.

9. Kumar A, Bennetzen JLJArog. Plant retrotransposons. 1999;33(1):479-532.

10. Novoselskaya-Dragovich AY, Fisenko AV, Konovalov FA, Mitrofanova OP, Shishkina AA, Kudryavtsev AMJGr, et al. Analysis of genetic diversity and evolutionary relationships among hexaploid wheats Triticum L. using LTR-retrotransposon-based molecular markers. 2018;65(1):187-98.

11. Hsu C-C, Chen S-Y, Lai P-H, Hsiao Y-Y, Tsai W-C, Liu Z-J, et al. Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids. 2020;21(1):1-13.

12. Jouffroy O, Saha S, Mueller L, Quesneville H, Maumus FJBg. Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening. 2016;17(1):1-15.

13. Natali L, Cossu RM, Mascagni F, Giordani T, Cavallini AJTG, Genomes. A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome. 2015;11(5):1-13.

14. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. 2014;111(14):5135-40.

15. Cho J, Benoit M, Catoni M, Drost H-G, Brestovitsky A, Oosterbeek M, et al. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. 2019;5(1):26-33.

16. Dooner HK, Wang Q, Huang JT, Li Y, He L, Xiong W, et al. Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions. 2019;116(22):10734-43.

17. Griffiths J, Catoni M, Iwaski M, Paszkowski J. Sequence-independent identification of active LTR retrotransposons in Arabidopsis. 2018.

18. Esposito S, Barteri F, Casacuberta J, Mirouze M, Carputo D, Aversano RJP. LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions. 2019;250(5):1781-7.

19. Cho J. Transposon-derived non-coding RNAs and their function in plants. Frontiers in plant science. 2018;9:600.

20. Campo S, Sánchez‐Sanuy F, Camargo‐Ramírez R, Gómez‐Ariza J, Baldrich P, Campos‐Soriano L, et al. A novel Transposable element‐derived microRNA participates in plant immunity to rice blast disease. 2021.

21. Akakpo R, Carpentier MC, Ie Hsing Y, Panaud OJNP. The impact of transposable elements on the structure, evolution and function of the rice genome. 2020;226(1):44-9.

22. Ma J, Devos KM, Bennetzen JLJGr. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. 2004;14(5):860-9.

23. Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, et al. Transposable elements contribute to dynamic genome content in maize. The Plant Journal. 2019;100(5):1052-65.

24. Mascagni F, Giordani T, Ceccarelli M, Cavallini A, Natali L. Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.). BMC genomics. 2017;18(1):1-16.

25. Qiu F, Ungerer MC. Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species. BMC plant biology. 2018;18(1):1-8.

26. Meyers BC, Tingey SV, Morgante M. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Research. 2001;11(10):1660-76.

27. Vukich M, Giordani T, Natali L, Cavallini A. Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.). BMC Plant Biology. 2009;9(1):1-12.

28. Kirov I, Omarov M, Merkulov P, Dudnikov M, Gvaramiya S, Kolganova E, et al. Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.). 2020;21(23):9331.

29. Nie Q, Qiao G, Peng L, Wen XJPP, Biochemistry. Transcriptional activation of long terminal repeat retrotransposon sequences in the genome of pitaya under abiotic stress. 2019;135:460-8.

30. Tiwari KS, Srivastava Y, Singh VK, Singh M, Singh BJVS. LTR retroelement in genes related to abiotic stress in Capsicum annuum L. 2017;44(2):1-7.

31. Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, Mittelsten Scheid OJPg. How a retrotransposon exploits the plant's heat stress response for its activation. 2014;10(1):e1004115.

32. Sabot F, Picault N, El‐Baidouri M, Llauro C, Chaparro C, Piegu B, et al. Transpositional landscape of the rice genome revealed by paired‐end mapping of high‐throughput re‐sequencing data. 2011;66(2):241-6.

33. Hirochika H. Contribution of the Tos17 retrotransposon to rice functional genomics. Current opinion in plant biology. 2001;4(2):118-22.

34. Cheng C, Daigen M, Hirochika HJMG, Genomics. Epigenetic regulation of the rice retrotransposon Tos17. 2006;276(4):378-90.

35. Chen J, Lu L, Benjamin J, Diaz S, Hancock CN, Stajich JE, et al. Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice. 2019;10(1):1-10.

36. Biémont C, Vieira C. Junk DNA as an evolutionary force. Nature. 2006;443(7111):521-4.

37. Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331-68.

38. Pearce S, Knox M, Ellis T, Flavell A, Kumar A. Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Molecular and General Genetics MGG. 2000;263(6):898-907.

39. Jiménez‐Ruiz J, Ramírez‐Tejero JA, Fernández‐Pozo N, Leyva‐Pérez MdlO, Yan H, Rosa Rdl, et al. Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.). 2020;13(1):e20010.

40. Qin Y, Shin K-S, Woo H-J, Lim M-H. Genomic variations of rice regenerants from tissue culture revealed by whole genome re-sequencing. Plant Breeding and Biotechnology. 2018;6(4):426-33.

41. Zhang R-G, Wang Z-X, Ou S, Li G-YJb. TEsorter: lineage-level classification of transposable elements using conserved protein domains. 2019:800177.

42. Katoh K, Standley DMJMb, evolution. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. 2013;30(4):772-80.

43. Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQJMb, evolution. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. 2015;32(1):268-74.

44. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution. 1980;16(2):111-20.

45. Ma J, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proceedings of the National Academy of Sciences. 2004;101(34):12404-10.

46. Jeon J-S, Chung Y-Y, Lee S, Yi G-H, Oh B-G, An G. Isolation and characterization of an anther-specific gene, RA8, from rice (Oryza sativa L.). Plant molecular biology. 1999;39(1):35-44.

47. Bolger AM, Lohse M, Usadel BJB. Trimmomatic: a flexible trimmer for Illumina sequence data. 2014;30(15):2114-20.

48. Langmead B, Salzberg SLJNm. Fast gapped-read alignment with Bowtie 2. 2012;9(4):357-9.

49. Liao Y, Smyth GK, Shi WJB. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. 2014;30(7):923-30.

50. Thorvaldsdóttir H, Robinson JT, Mesirov JPJBib. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. 2013;14(2):178-92.

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Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

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