Skip to main content
PMC home page
G3: Genes | Genomes | Genetics logoLink to G3: Genes | Genomes | Genetics
. 2017 Apr 14;7(6):1875–1885. doi: 10.1534/g3.116.037572

Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species

Qun-Jie Zhang *,†,‡, Li-Zhi Gao *,1
PMCID: PMC5473765  PMID: 28413161

Abstract

The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice.

Keywords: LTR retrotransposons, Oryza, AA-genome, rice speciation, comparative genomics

LTR retrotransposons are major components of plant genome modification and reorganization (Bennetzen 2000; Jiang and Ramachandran 2013; Wessler et al. 1995). As one of the longest classes of transposable elements, their abundance makes them an important driver of plant genome size variation (Piegu et al. 2006; Vitte and Panaud 2005). For instance, the Arabidopsis thaliana genome (∼157 Mb) has a very limited number of LTR retrotransposons, 5.60% (Pereira 2004), the rice genome (∼389 Mb) is comprised of ∼22% LTR retrotransposon sequences (Ma et al. 2004), and 74.6% of the maize genome (2045 Mb) is occupied by LTR retrotransposon elements (Baucom et al. 2009a). Moreover, both LTR reverse transcriptase (RT) activity and the host genome together help to restrain mechanisms such as their deletion, unequal recombination, and methylation, which affect the overall abundance of LTR retrotransposons (Bennetzen 2002; Petrov et al. 2000; SanMiguel et al. 1998; Vitte and Panaud 2003). Differential retrotransposition activity and DNA loss rates affect the half-life of LTR retrotransposons in different plant species; wheat and barley, for example, were found to have far longer periods of retrotransposon activity when compared to rice (Wicker and Keller 2007). The nature and dynamic changes of LTR retrotransposons during the speciation process are poorly understood.

The structure of LTR retrotransposons is similar to retroviruses (Xiong and Eickbush 1990), encoding for two proteins: gag and pol. Previously, the position of the RT gene in relation to the integrase (IN) gene of pol was used to classify the retrotransposon families into Ty1-copia (PR-IN-RT) and Ty3-gypsy (PR-RT-IN), respectively (Coffin et al. 1997; Eickbush and Jamburuthugoda 2008). Extensive investigations in diverse plant genomes have shown that at least six ancient Ty1-copia and five Ty3-gypsy lineages existed before the divergence of monocots and dicots (Du et al. 2010; Wang and Liu 2008). Recent studies have revealed considerable differences in the proportion of Ty1-copia and Ty3-gypsy elements among many plants, such as maize (Baucom et al. 2009a), Medicago truncatula (Wang and Liu 2008), Populus trichocarpa (Cossu et al. 2012), Orobanche, and Phelipanche (Piednoel et al. 2013), consistent with their role in determining genome size variation. In addition, a large proportion of LTR retrotransposons are comprised of nonautonomous elements (Wawrzynski et al. 2008), the replication of which relies completely, or at least in part, on proteins expressed by other elements elsewhere in plant genomes (Vitte and Panaud 2005). In the rice genome, for example, Dasheng and RIRE2 were previously characterized as a nonautonomous LTR retrotransposon family and its putative autonomous partner, respectively. Both types of retrotransposon elements have similar patterns of chromosomal distribution and target site sequences (TSD), suggesting that they use the same transposition machinery and are likely coexpressed (Jiang et al. 2002). Individual retrotransposon families usually have their own amplification histories, the majority of which exhibit an increased rate of transposition at different periods during the evolutionary process (Baucom et al. 2009b; Vitte et al. 2007; Wicker and Keller 2007). Specific LTR retrotransposon families, thus, expand at distinct evolutionary periods, because some families are especially prone to be more active than others until mutated (Estep et al. 2013). Comparisons of closely related plant species are important to refine burst rates, molecular evolution, and patterns of LTR retrotransposon changes during and after speciation.

The availability of rice reference genome sequences has offered an unparalleled opportunity to understand the evolution of plant retrotransposons, including retrotranspositional dynamics, the rates of amplification and removal of the LTR retrotransposons, as well as natural selection within LTR retrotransposon families in the rice genome (Baucom et al. 2009b; Ma et al. 2004; Tian et al. 2009; Vitte and Panaud 2003). Comparative genomic analyses among multiple divergent plant lineages have provided considerable insight into the conservation and evolutionary dynamics of ancient retrotransposon lineages (Jiang and Ramachandran 2013; Roulin et al. 2009; Wicker and Keller 2007). Besides which, a large number of whole genome-based studies have yielded a comprehensive understanding of the evolution of LTR retrotransposons in flowering plants such as Arabidopsis, rice, soybean, Medicago, and maize (Wicker and Keller 2007; Baucom et al. 2009a,b; Du et al. 2010; Wang and Liu 2008). However, to our knowledge, little is known about genome-wide patterns of the gain and loss of recently amplified LTR retrotransposons and evolutionary birth and death processes of different families among closely related plant species. In this regard, comprehensive comparisons of very closely related plant species that span the speciation continuum and diverged close to the period of half-life of LTR retrotransposons would significantly improve the inference precision and sensitivity of LTR retrotransposon evolution.

The genus Oryza serves as an ideal group fulfilling the requirement to study the recent evolution of LTR retrotransposons. They comprise ∼21 wild and 2 cultivated species, which can be classified into 10 distinct genome types (AA, BB, CC, EE, FF, GG, BBCC, CCDD, HHJJ, and HHKK) (Aggarwal et al. 1997; Ge et al. 1999). Among them, Oryza australiensis (EE genome, ∼965 Mb) has the largest genome size, nearly doubling its genome size by accumulating over 90,000 retrotransposons (Piegu et al. 2006). On the contrary, O. brachyantha (FF genome, ∼261 Mb) has the smallest genome size with a limited number of retrotransposons (Chen et al. 2013; Uozu et al. 1997). The AA-genome Oryza species, also called the O. sativa complex, consist of two cultivated rice species, Asian cultivated rice (O. sativa) and African cultivated rice (O. glaberrima), and six wild rice species (O. rufipogon, O. nivara, O. barthii, O. glumaepatula, O. longistaminata, and O. meridionalis), which are disjunctively distributed in pantropical regions of the four continents of Asia, Africa, South America, and Australia (Vaughan 1989; Vaughan et al. 2003). The recent phylogenomic analysis of these eight diploid AA-genome species supports a series of closely spaced speciation events in this genus (Zhu et al. 2014). Previous studies have identified numerous LTR retrotransposon families that were found to have undergone bursts of amplification within the last 5 MY in the O. sativa genome (Matyunina et al. 2008). Such a time scale seems older than the earliest divergence time estimated for the split from a common AA-genome ancestor ∼4.8 MY (Zhu and Ge 2005; Zhu et al. 2014).

Here, we perform a genome-wide comparison in a phylogenetic context, and characterize the evolutionary dynamics of LTR retrotransposons across eight completed or nearly finished AA-genomes of the Oryza (Zhang et al. 2014). Our study has, for the first time, fully reconstructed the evolutionary history of LTR retrotransposon families in closely related rice species. These data provide a starting point for the exploration of how evolutionary dynamics of LTR retrotransposons can strongly influence plant genome size variation and genome evolution during the process of recent plant speciation.

Materials and Methods

Eight genome sequences of Oryza AA-genome species

The genomic sequences of O. sativa ssp. japonica. cv. Nipponbare (Release 7) (abbreviated as SAT) were downloaded from http://rice.plantbiology.msu.edu. The draft genomes of the other seven AA-genome Oryza species of O. rufipogon (RUF), O. nivara (NIV), O. glaberrima (GLA), O. barthii (BAR), O. glumaepatula (GLU), O. longistaminata (LON), and O. meridionalis (MER) were recently sequenced and published (Zhang et al. 2014).

Annotation and classification of LTR retrotransposon elements

We performed de novo searches for LTR retrotransposons against the eight rice genome sequences using LTR_STRUC (McCarthy and McDonald 2003). False positives caused by long tandem repeats were manually removed by BLAST searches. All intact LTR retrotransposons were classified into Ty1-copia, Ty3-gypsy, and unclassified groups according to the order of ORFs using PFAM (Finn et al. 2008). The RT sequences were retrieved from each retrotransposon element and further checked by homology searches against the published RT genes available from GyDB (http://gydb.org/) (Llorens et al. 2011). They were aligned using ClustalW (Larkin et al. 2007) and manually curated (Table 1). Previous LTR retrotransposon family nomenclature (see Figure 1 and Figure 2) was determined using BLAST searches with LTR retrotransposons downloaded from TIGR (Ouyang and Buell 2004) and Repbase (Jurka 1998, 2000; Jurka et al. 2005). A homology search of the genome sequence was performed using RepeatMasker (Smit et al. 1996–2010). All intact LTR retrotransposon sequences generated by LTR_STRUC (McCarthy and McDonald 2003) were classified into families using BLASTClust (http://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html) and all-to-all BLAST of 5′-LTR sequences, followed by manual inspection (Llorens et al. 2011). The family classification standard was considered acceptable if >50% of the 5′-LTRs and sequence identity was >80%. Detailed information of LTR retrotransposon families is provided in Supplemental Material, Table S1 in File S1.

Table 1. Statistics of the LTR retrotransposons in the eight AA-genome Oryza species.

Total SAT RUF NIV GLA BAR GLU LON MER
Assembled lengtha 373 394 307 312 308 305 298 311
Estimated lengthb 389 473 395 370 376 366 344 388
Numbers of LTR retrotransposon families
 Total 790 582 733 641 643 606 634 698 649
 Ty1-copia 126 104 123 113 108 107 116 114 113
 Ty3-gypsy 166 132 155 131 136 125 133 149 138
 Unclassified 498 346 455 397 399 374 385 435 398
Sequence lengths of retrotransposons in the genomesc
 Total 124.02 97.32 76.88 78.13 74.97 74.73 62.83 80.67
 Ty1-copia 12.65 10.94 8.86 8.97 8.59 8.92 6.61 9.49
 Ty3-gypsy 66.63 39.01 30.02 30.82 28.75 29.14 20.87 33.43
 Unclassified 44.73 47.37 38.00 38.34 37.62 36.67 35.35 37.75
Open in a new tab

SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7); RUF, O. rufipogon; NIV, O. nivara; GLA, O. glaberrima; BAR, O. barthii; GLU, O. glumaepatula; LON, O. longistaminata; MER, O. meridionalis; LTR, long terminal repeat.

a

Assembled length (Mb) stands for total contig length.

b

Estimated length (Mb) was assessed by reads at 17 k-mer.

c

Sequence lengths of LTR retrotransposons in genomes (Mb) were calculated based on the annotation using RepeatMasker.

Figure 1.

Figure 1

Open in a new tab

Insertion times and read depth analysis of the top 23 LTR retrotransposon families. (A) Insertion times of the exemplar LTR retrotransposons from SAT. Black circles indicate mean values, black bars signify 25–75% of values, dark gray lines represent 5–95% of values, and green circles denote extreme values. The light gray horizontal lines show divergence times between SAT and the other seven species. Those inserted earlier than 5 MY are set at ∼5 MY. Ty3-gypsy (red dots) Ty1-copia (blue dots) elements are distinguished. (B) Heatmap of the proportions of LTR read depth compared within each family across the eight rice genomes. BAR, O. barthii; GLA, O. glaberrima; GLU, O. glumaepatula; LON, O. longistaminata; LTR, long terminal repeat; MER, O. meridionalis; MY, million years; Mya, million years ago; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

Figure 2.

Figure 2

Open in a new tab

Phylogenetic trees of representative LTR retrotransposon lineages across the eight AA-genome Oryza species. Neighbor joining and unrooted trees were constructed based on sequences of RT genes for Ty1-copia (A) and Ty3-gypsy (B). The backbone of the RT trees and retroelements from SAT are shown in black, while colored branches indicate those from other seven species. LTR retrotransposons from NIV and RUF (the closest to SAT), GLA and BAR (similar divergence time to SAT), GLU, LON, and MER are colored in red, orange, green, light blue, and dark blue, respectively. BAR, O. barthii; GLA, O. glaberrima; GLU, O. glumaepatula; LON, O. longistaminata; LTR, long terminal repeat; MER, O. meridionalis; MY, million years; Mya, million years ago; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RT, reverse transcriptase; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

Dating LTR retrotransposon elements

Dating LTR retrotransposons assumes that the two LTRs were identical when they inserted into the host genome (SanMiguel et al. 1998). The insertion times of intact LTR retrotransposon elements were calculated based on a previously published approach (SanMiguel et al. 1998). The two LTRs of each intact LTR retrotransposon that contains a TSD were aligned using ClustalW (Larkin et al. 2007) and their nucleotide divergence was estimated using the baseml module implemented in PAML (Yang 2007). The insertion times were then computed using T = K/2r, where T = insertion time, r = synonymous mutations/site/MY, and K = the divergence between the two LTRs. A substitution rate of 1.3 × 10−8 per site per year was used to calculate insertion times (Baucom et al. 2009b; Vitte et al. 2007).

Phylogenetic analysis

Nucleotide sequences of RT domains were retrieved from the intact LTR retrotransposon elements of SAT. For the other seven species, RT sequences were also included that were annotated by RepeatMasker (Smit et al. 1996–2010), following the guidelines set forth by Xiong and Eickbush (1990). Sequence alignments of amino acid sequences of the RT regions were performed by using ClustalW2 (Larkin et al. 2007) and were adjusted manually. The neighbor joining method was used to generate unrooted trees using uncorrected pairwise distances from the sequence alignments with the program MEGA 6 (Tamura et al. 2007). In total, 2420 Ty3-gypsy and 983 Ty1-copia RT sequences were extracted to construct phylogenetic trees. For convenience, we only display tree topologies using 414 Ty3-gypsy and 447 Ty1-copia retroelements (Figure 2) after removing highly similar sequences. These Ty3-gypsy and Ty1-copia RT sequences were classified into 11 lineages, consistent with previous results (Hřibová et al. 2010; Llorens et al. 2009; Vitte et al. 2007; Wicker and Keller 2007). The RT sequences of SAT were all derived from intact LTR retrotransposons. In the other seven species, besides intact LTR elements, we included partial RT sequences annotated by RepeatMasker (Smit et al. 1996–2010).

Read depth analysis

To investigate the abundance and evolutionary dynamics of the LTR retrotransposon families, we performed read depth analysis to estimate LTR retrotransposon copy number. The libraries of reference LTRs were constructed using the output from both LTR_STRUC (McCarthy and McDonald 2003) and RepeatMasker (Smit et al. 1996–2010) for each species after removing sequence redundancy using cd-hit-est (Fu et al. 2012; Li and Godzik 2006) at an identity cutoff of 0.95 (Zhang et al. 2006). Some highly similar genomic regions failed to be assembled for the seven draft AA-genome sequences using Illumina sequencing technology. Approximately fivefold sequence coverage of Illumina 100 PE reads from each species were randomly sampled and mapped to each reference LTR by SOAPaligner/soap2 (Li et al. 2009). Actual read depths for each LTR were estimated by dividing the depths obtained by the average read depth for the whole genome. For uncertain reads mapping between LTRs and inner regions, only LTR depths were computed to estimate the abundance of the representative families. Considering that truncated reference LTRs may influence the estimation of mapping depths, LTRs shorter than 150 bp were excluded. We determined that LTRs shorter than 150 bp, in part, belonged to Ale of Ty1-copia, while others were members of unclassified families; most of these were single-copy families and had been silenced within the last 3 MY.

Data availability

The authors state that all data necessary for confirming the conclusions presented in the article are represented fully within the article.

Results and Discussion

Genome-wide assessment of LTR retrotransposon abundance

To discover the abundance of LTR retrotransposons across all eight AA-genome Oryza species, we characterized these elements using an integrated approach that considers both structure and homology, as described in Materials and Methods. Besides the SAT genome (Release 7, IRGSP, http://www.ncbi.nlm.nih.gov), seven recently completed draft AA-genomes (Zhang et al. 2014) were used in this study, including RUF, NIV, GLA, BAR, GLU, LON, and MER. The order of the species used in this study reflects the topology of the phylogenetic tree that we recently reconstructed (Zhu et al. 2014). Our retroelement discovery process yielded a total of 3911 intact LTR retrotransposons in the eight rice genomes after removing ∼30 redundant elements. Our definition of an intact retrotransposon element defines it as a copy that has both complete LTR ends, but does not make any statement of whether it encompasses internal insertions or deletions. These intact elements were subsequently clustered into different families using BLASTClust and all-to-all BLAST (Llorens et al. 2011) (Table S1 in File S1). We define a “family” based on 5′-LTR sequence identity. Because LTRs do not encode proteins, they are among the most rapidly evolved sequence regions of the retrotransposons. We consider two retroelements as belonging to the same family if their LTR sequence identity exceeds 80% and they show 50% reciprocal overlap in their lengths. Note that these criteria are somewhat stricter than those reported in other studies (Baucom et al. 2009b; Seberg and Petersen 2009) and looser than that proposed by Wicker et al. (2007), as we aimed to detect the variation and divergence of LTR retrotransposon families among these closely related species. As a result, we could classify intact rice LTR retrotransposon elements into a total of 790 families, of which there were 99 multi-member families with >2 intact copies and 160 single-member families in SAT. The remaining 531 families including both single- and multi-members were identified among the other seven non-SAT genomes. This suggests the generation and expansion of a large number of retrotransposon families after the divergence of SAT and non-SAT genomes. Using PFAM (Finn et al. 2008) and tBlastN (1e−10, coverage ≥30%), we further grouped them into 126 Ty1-copia families comprising 775 intact elements and 166 Ty3-gypsy families with 1803 intact elements. The other 498 families, which include 1333 intact elements that lack the pol gene, were categorized as unclassified families (Table 1 and Table S1 in File S1). Even though there are fewer Ty3-gypsy families than Ty1-copia, Ty3-gypsy occur more prevalently than Ty1-copia elements in these eight rice genomes, as observed on SAT alone and the FF-genome species O. brachyantha (Chen et al. 2013). We operationally named family IDs by the number of the intact elements in SAT combined with the initials of the Oryza AA-genome of LTR retrotransposons (OAL) (i.e., OAL001, OAL002, OAL003, and so on). Of these identified multi-copy families, a total of 31 were previously described, and thus their corresponding family names used in earlier references are also provided in Table S2 in File S1. Our results show that the majority of families, if not all, are shared by all eight rice genomes, but their copy number varies dramatically among the species. More LTR retrotransposon families were identified among non-SAT genomes, despite the higher assembly quality of the SAT reference genome. The data ensures broad LTR retrotransposon representation necessary to study their diversity and evolution. The largest number of LTR retrotransposon families was detected in RUF followed by LON, consistent with known differences in genome size. To investigate the proportion of LTR retrotransposon sequence within these eight AA-genomes we also annotated their sequence length using RepeatMasker (Smit et al. 1996–2010). Although fewer LTR retrotransposon families are detected in SAT, the overall content of LTR retrotransposons in SAT was greater than any of the other seven genomes, likely due to the better assembly quality as a reference genome and the inherent difficulty of assembling full-length LTR retrotransposons in non-SAT genomes with NGS technology.

To assess retrotransposon expansion and contraction across the eight AA-genome Oryza species, we performed a read depth analysis of all identified retrotransposon families against their own assembled genomes. To test the reliability of read depth to estimate retrotransposon copy number variation, we compared the observed genome copy number of intact elements and LTR sequence read depth in SAT (Figure S1A in File S1). The results reveal that the number of intact elements significantly correlates with LTR read depth (r = 0.496, P < 0.01), and that LTR read depth may serve as a good proxy to evaluate LTR retrotransposon abundance. Read depth analysis of the most abundant 44 families measured by copy number further showed a significant correlation of SAT LTR read depth with each of the other seven species (Figure S1B in File S1). Taken together, our results suggest that LTR retrotransposon families experienced rapid diversification after the recent spilt of these eight AA-genome Oryza species over the past 4.8 MY.

Early integration of most LTR retrotransposon families before the split of rice species

When a retrotransposon element integrates into the host genome, the two LTR sequences are assumed to be identical. Thus, we may estimate the insertion times of LTR retrotransposons based on the sequence divergences between LTR pairs. Because the LTR sequences evolve more rapidly than genes, we employed an average substitution rate (r) of 1.3 × 10−8 substitutions per synonymous site per year to estimate insertions times (Ma et al. 2004). LTR sequences of the 3911 complete LTR retrotransposons from the most abundant 44 families were sampled to calculate their integration times (Table S1 in File S1). To trace when these retrotransposon elements came into the eight AA-genomes we searched and annotated overall features of the top 23 of these 44 retrotransposon families. In total, 2213 complete retrotransposon elements were dated by LTR identity and projected onto a phylogenetic tree of the eight AA-genome Oryza species (Figure 1). Our results show that almost all high-copy families, except for OAL011, could be detected and that the earliest insertion events for 18 families occurred before the AA-genome Oryza species diverged. The other five retrotransposon families appear to be younger, but may have lost more ancient LTR retrotransposon signatures due to a high turnover or interlocus gene conversion that destroys or homogenizes LTR retrotransposon structure. Others, such as OAL011, likely represent recently expanded retrotransposon families.

Phylogenetic trees of 11 representative retrotransposon lineages were constructed based on conserved RT domains for both Ty1-copia and Ty3-gypsy elements (Figure 2). Our results showed that, besides the majority of newly identified families in this study, the previously characterized LTR retrotransposon families including Ty1-copia and Ty3-gypsy could be found in all eight AA-genome Oryza species (Figure 2) (Du et al. 2010; Wang and Liu 2008; Wicker and Keller 2007), suggesting their early integration into the common ancestral genome. Of these 790 families, we identified 374 solo and full-length LTRs that were shared among these rice species. Only 26 that belong to single-copy families may be species-specific, while others were members of unclassified retrotransposon families (Table S1 in File S1). The majority of the LTR retrotransposon families came to the most recent ancestral genome before the divergence of all eight AA-Oryza genomes.

Evolutionary landscape of Ty1-copia and Ty3-3gypsy retrotransposons

Phylogenetic analyses of 11 representative retrotransposon lineages further show the evolutionary dynamics of rice LTR retrotransposons, including Ty1-copia (TAR, Ivana, Maximum, Ale, Bianca, and Angela) (Figure 2A) and Ty3-gypsy (Tat, Athila, Reina, CRM, and Tekay) (Figure 2B). Sequence lengths were calculated for each retrotransposon lineage using Repeatmasker (Smit et al. 1996–2010) and then compared across these rice genomes to characterize their content and contribution to genome size variation (Figure S2, A and B in File S1). Since the genome assembly quality may affect genome annotation, we specifically generated the histograms of total length in SAT as a control (Figure 3, A and B), revealing a consistent pattern in comparison with the other seven non-SAT draft genomes. Considering the difficulty of assembling newly amplified retrotransposons in these non-SAT genomes due to high sequence similarity, we complemented this analysis by LTR read depth estimates (Figure 3, C and D). The integrated data provide a more comprehensive framework for assessing how Ty1-copia and Ty3-gypsy retrotransposon elements recently amplified and diverged across the eight Oryza AA-genomes.

Figure 3.

Figure 3

Open in a new tab

Sequence features of Ty1-copia and Ty3-gypsy retrotransposon families across the eight AA-genome Oryza species. Total sequence of Ty1-copia (A) and Ty3-gypsy (B) elements in the SAT genome, annotated using RepeatMasker. LTR reads depth proxy for copy number for various Ty1-copia (C) and Ty3-gypsy (D) families. LTR, long terminal repeat; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

Phylogenetic analysis reveals that Ty1-copia families are more evolutionarily dispersed and smaller in size than Ty3-gypsy, consistent with previous reports (Vitte et al. 2007). Note that long branches represent early retrotransposon insertions, whereas short clusters indicate new bursts. It is clear that TAR possesses a large number of newly generated SAT retrotransposon families, for example, OAL007 (Houba) and OAL013 (osr1 and osr5) (Figure 2A). Although the copy number TAR was moderate (based on read depth), the insert length was relatively large in comparison to other Ty1-copia lineages, consistent with an increased number of recently amplified intact retroelements (Figure 3A and Figure S2A in File S1). Compared to non-SAT genomes, Angela and Ivana families drive the latest burst of retrotransposons in SAT. It is interesting to note that the majority of LTR retrotransposons in Ale may represent ancient retrotransposon amplification events, as they formed the largest number of long branches in the Ty1-copia phylogenetic tree. Both the total length and read depth of the Maximus lineage are relatively large, especially in RUF, indicating a substantial contribution to the increase in genome size. In contrast to Maximus, Bianca was reported to have become extinct in soybean (Du et al. 2010). This was exemplified by the longest phylogenetic branch lengths (Figure S2A in File S1), and the shortest insert lengths in the eight rice genomes (Figure 3, A and B and Figure S2A in File S1).

Compared to Ty1-copia (Gao et al. 2004), Ty3-gypsy retrotransposon elements serve as an important driver of rice genome evolution due to their longer sequence lengths and more recent rounds of amplification. Thus, even though there are fewer Ty3-gypsy families than Ty1-copia, Ty3-gypsy are more prevalent than Ty1-copia elements in this set of rice genomes when compared to SAT alone (McCarthy et al. 2002), and the FF-genome species O. brachyantha (Chen et al. 2013). Phylogenetic analysis not only confirms recent bursts of Ty3-gypsy retrotransposon elements in SAT (McCarthy et al. 2002) but also reveals recent amplification of diverse families, usually shown by grouping numerous short branches together across these rice genomes (Figure 2B). Tat represents such an example and comprises several newly amplified retrotransposon families, such as OAL002, OAL003, OAL005, and OAL008 (Figure 2B). The total lengths of Tat retroelements are apparently higher than any other Ty3-gypsy lineages, probably resulting from the high copy number of intact elements (Figure 3, B and D and Figure S2B in File S1). Tekay typifies the most prevalent group of retrotransposons (e.g., OAL001) (Figure 2B, Figure 3, B and D, and Figure S2B in File S1). New bursts of OAL001, specifically in SAT and RUF, are far more abundant than any of the other six rice species (Figure 2B, Figure 3, B and D, and Figure S2B in File S1). Reina shows the greatest number of long branches, represented by all eight species, indicating their early integration into the common ancestral genome (Figure 2B). The observation of a high LTR retrotransposon copy number (Figure 3D) but short insert lengths for Reina (Figure 3D and Figure S2B in File S1) suggests that highly fragmented single-copy elements persist in these rice genomes. The remaining two lineages, Athila and CRM, show low levels of retrotransposition with both small inset lengths and low numbers of LTR retrotransposons.

Our results show that, in contrast to Ty1-copia elements, species-specific bursts of the five Ty3-gypsy lineages more frequently occurred and thus more actively drove genome evolution after the recent speciation of these rice species. Rapid amplification of Tekay is restricted to SAT and RUF, Tat quickly amplified in RUF but was inactive in BAR, and recent Reina bursts are observed in BAR and LON. As for Ty1-copia lineages, only Maximus shows evidence of bursts in RUF, LON, and MER. By following recent speciation, independent rapid amplifications of LTR retrotransposon lineages have occurred leading to remarkably differing sequence content in these rice genomes. Bursts of Tat, Tekay, and Maximum retrotransposons, for instance, have resulted in an estimated increase of genome size of ∼100 Mb in RUF ∼0.72 MYA (million years ago) (Zhu et al. 2014), while lineage-specific accumulation of retrotransposons (e.g., Reina) has occurred between GLA and its wild progenitor BAR, which split ∼0.26 MYA (Zhang et al. 2014). Moreover, recent bursts of one or more retrotransposon lineages appear to have frequently occurred in specific species: Tekay in SAT; Tat, Tekay, and Maximum in RUF; Reina in BAR; Reina and Maximum in LON; and Maximum in MER.

Demographic history of rice retrotransposon families

Comparative analysis of the eight complete rice genomes allow us, for the first time, to trace the life history of retrotransposon families in closely related plant species. Although it is difficult to accurately date the earliest insertion events of a retrotransposon family, the burst periods for each family may be followed by examining the distribution of insertion times (Figure 1). Of the top 23 most abundant retrotransposon families in this study, we found that 11 are still active with at least one element having two identical LTRs; the other 12 have completed their entire life histories during an earlier period when AA-genomes diverged. There are typically lower proportions of these elements in SAT when compared to one or more of the other AA-genome species.

From an evolutionary perspective, the accumulation of these retrotransposon families varied dramatically among the lineages (Figure 1). Highly amplified retrotransposon families (e.g., OAL005, OAL006, OAL008, OAL010, and OAL012) shared a relatively short half-life when compared to those with fewer retrotransposition events that evolved during similar periods (e.g., OAL015, OAL016, OAL017, OAL018, and OAL019). OAL021 experienced a rapid proliferation of copy number but the shortest life history; nearly all insertions occurred within ∼0.2 MY, approximately equal to when GLU split from the common ancestor of SAT/RUF/NIV and GLA/BAR. The retrotransposition activity of this family declined rapidly during the next 0.2 MY within the SAT lineage. These results suggest that high levels of retrotransposition activity may be associated with strong negative selection, special environmental stresses, or other random events (Grandbastien 1998; Grandbastien et al. 2005).

In order to understand the evolutionary dynamics of rice LTR retrotransposons in the context of their insertion times, we classified a total of 2326 intact retroelements from 261 SAT families into high-copy (>20), low-copy (2–20), and single-copy families. Estimation of insertion times suggests that single-copy retrotransposon elements, followed by low-copy families, populated their host genome quite early (∼1–10 MYA). The majority of these are incomplete with respect to their LTR retrotransposon structure (Figure S3A in File S1), but homology searches gleaned a number of retrotransposon fragments in SAT and the other seven rice genomes as well. Our calculation of proportions of LTR retrotransposon sequence lengths revealed that high-copy number families possess ∼2/3 of the total sequence length, far more than low- and single-copy number families (Figure S3B in File S1).

The OAL008 family typifies the evolutionary history of a common LTR retrotransposon across the eight rice species (Figure S4A in File S1). The normal distribution of insertion times of OAL008 retrotransposons shows no evidence of any new insertions within the last 0.5 MY; OAL008 came into the host genome and began to amplify before the AA-genome Oryza species diverged about ∼4.8 MYA. It reached its zenith ∼1–2 MYA in SAT. The time span from initial insertion to the burst was relatively longer than the period from the burst to the inactivity of retrotransposition. Our data confirm that the half-life of this family is ∼4 MY in AA-genome Oryza species, which is quite consistent with previous estimates of ∼3–4 MY in SAT (Ma and Bennetzen 2004; Vitte et al. 2007). Phylogenetic analysis of the OAL008 retroelements based on RT alignment of 155 amino acid sequences shows an almost uniform growth of species-specific retrotransposons among these species (Figure S4A in File S1); LTR retrotransposon copy number analysis indicates that OAL008 was more abundant in RUF and MER than in the other six species (Figure 1).

Since the average retrotransposon half-life is ∼4 MY in rice, LTR retrotransposon insertions older than that frequently become highly fragmented, consistent with a pattern of speedy accumulation, decline, and extinction. Our study has revealed novel insights into the evolutionary dynamics of retrotransposons: After new retrotransposon lineages are generated and begin to integrate into their host genome, some may immediately adopt a normal life-history involving several rounds of burst, accumulation, and decline, producing a large number of elements. Others survive and amplify at different rates and then gradually degenerate, or become dormant amplifying at a later date before becoming eliminated. Retrotransposon maintenance and potential is thought to be largely determined by mechanisms such as deletion, unequal recombination, and methylation (Bennetzen 2002; Petrov et al. 2000; SanMiguel et al. 1998). LTR retrotransposons experience high levels of mutation, rearrangement, and recombination, providing a rich genetic resource for the generation of new LTR retrotransposon elements (Dolgin and Charlesworth 2008; Ma and Bennetzen 2006). Under conditions of environmental change, or especially biotic and abiotic stresses that serve as strong forces of natural selection, some LTR retrotransposons that manage to escape suppression from the host genome may become a new burst branch (Baucom et al. 2009b; Grandbastien 1998). However, more examples, as well as experimental evidence, are required to reveal the precise conditions that may stimulate rapid amplifications of some retrotransposon families while suppressing others to produce such a large number of low-copy or single-copy families in host genomes.

Lineage-specific massive LTR retrotransposon bursts in very recently diverged AA-genome Oryza species

The significant correlation of the top 44 most abundant retrotransposon families between SAT and each of the other seven species may indicate that these genomes have experienced a rapid amplification of genome-wide LTR retrotransposons. However, LTR copy number analysis indicates that certain families massively amplified in a lineage-specific manner (Figure S1B in File S1) and, thus, underwent distinct evolutionary paths since the recent split of AA-genome Oryza species over the past ∼4.8 MY (Ma and Bennetzen 2006). To exemplify the idiosyncratic nature of these expansions, we present the findings of the top three most abundant retrotransposon families: OAL001, OAL002, and OAL003.

OAL001 represents the largest family, including the three previously reported retrotransposon families in rice: RIRE3, RIRE8, and Osr34. A total of 385 OAL001 retrotransposons group into three clusters based on a phylogenetic analysis of LTRs (Figure 4A), which is further supported by analysis of the RT sequences (I, II, and III) (Figure 4B). Detailed analysis of the LTR phylogenetic tree shows that this family contains the three Ty3-gypsy branches (I, II, and III) and one nonautonomous branch (IV). It is clear that branch IV is derived from branch III; the nonautonomous branch IV shows the fewest copy numbers in SAT and possesses highly homologous but longer LTRs from autonomous branches due to insertions (Figure 4C). LTR read depth analysis suggests vast bursts of all four branches of the OAL001 family, but only in SAT and RUF and not the other six species (Figure 4D). Note that both RUF and NIV are the presumed wild progenitor of SAT; although extensive population sampling of RUF, NIV, and SAT is required to further refine the evolutionary dynamics and mechanisms behind this species continuum. Our data support a very recent and massive burst of this largest retrotransposon family immediately after the fairly recent speciation of SAT, NIV, and RUF.

Figure 4.

Figure 4

Open in a new tab

Evolutionary dynamics of the OAL001 family across the eight AA-genome Oryza species. (A) Phylogram based on LTRs and (B) RT sequences; (C) genomic structure of retroelements across the four branches in OAL001; (D) read depth analysis of each of the four branches in the eight species: branch I (yellow), branch II (green), branch III (blue), and the nonautonomous branch IV (pink). White dots indicate unclassified retrotransposon families. BAR, O. barthii; GLA, O. glaberrima; GLU, O. glumaepatula; LON, O. longistaminata; LTR, long terminal repeat; MER, O. meridionalis; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RT, reverse transcriptase; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

OAL002 is a Ty3-gypsy family formerly known as hopi, with full-length insertions of up to 12 kb (Picault et al. 2009). Given the relatively long sequence length for each intact element, the growth and decay of a retrotransposon family like OAL002, at least to some extent, has influenced the genome size of AA-genome Oryza species. Phylogenetic analyses of both RT (N = 375) and LTR (N = 373) sequences clearly cluster the retrotransposon elements into two groups (I and II) (Figure 5A). Interestingly, the estimation of insertion times suggests that group I elements are ancient (older than 7 MY) but experienced only small amplification events after they separated from the other Tat families ∼2.5–1 MYA (Figure 5B). After a short epoch of silence, massive bursts of retrotransposons (group II) rapidly occurred in SAT, RUF, and NIV ∼1 MYA, a time equivalent to the divergence of Asian SAT, RUF, and NIV from other AA-genome Oryza species (Figure 5B). Such an ongoing amplification of these three Asian rice species (RUF, SAT, and NIV) has contributed a large proportion of OAL002 retrotransposons when compared to the other five rice species.

Figure 5.

Figure 5

Open in a new tab

Evolutionary dynamics of the OAL002 family across the eight AA-genome Oryza species. (A) Phylogenetic trees constructed using RT gene and 5′-LTR sequences, respectively. (B) Distribution of insertion times. The burst of LTR retrotransposon elements that occurred in the Asian lineage (SAT, RUF, and NIV) are highlighted (pink) in contrast to those shared by all eight AA-genome Oryza species (blue). The burst of LTR retrotransposons is largely restricted to SAT. Myr, million years; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RT, reverse transcriptase; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

OAL003 contains two renowned families, Dasheng and RIRE2, which have been studied extensively, serving as an excellent model to explore evolutionary relationships between autonomous and nonautonomous retrotransposon elements in plants (Grandbastien et al. 2005; Jiang et al. 2002). Phylogenetic analysis of 930 LTR sequences cluster OAL003 retrotransposons into the eight branches (I, II, III, IV, V, VI, VII, and VIII) that separated earlier than the divergence of the eight AA-genome Oryza species. Among these, the two most prevalent clades, I and VIII, are equal to Dasheng and RIRE2, respectively (Figure 6A). Previous studies in rice incorporated III, IV, V, and VI into an “intermediate” group between Dasheng and RIRE2 using the long branch II as the outgroup; these studies also reported that Dasheng and RIRE2 share similar insertion sites and observed some chimeric Dasheng/RIRE2 elements (Jiang et al. 2002). In this study, we estimated the number of insertion events and the evolutionary origin of these two groups. Our analysis reveals that the number of nonautonomous Dasheng elements has gradually exceeded that of donor RIRE2 elements over the last 0.5 MY (Figure 6B). This tendency may have limited retrotransposon efficiency by reducing the supply of enzymes needed for a successful retrotransposition. Our results show that, in comparison to other AA-genome species, OAL003 retrotransposons became exceptionally amplified in RUF (Figure 6, A and C). It is apparent that the RUF genome possesses a large quantity of RIRE2 relative to Dasheng, promoting higher RT activity (Figure 6A). The mechanisms involved in the enzyme capture and subsequent reverse transcription between Dasheng and RIRE2 still remain unknown. However, the competition between nonautonomous elements and their donors may conceivably explain these potential differences of reverse transcription activity in rice.

Figure 6.

Figure 6

Open in a new tab

Evolutionary dynamics of the OAL003 family across the eight AA-genome Oryza species. (A) Radial phylogram clusters OAL003 LTR retrotransposon family into seven clades with the relative proportion by species (see (C) for color key) indicated by the pie chart. The two most prevalent two clades are I (Dasheng) and VII (RIRE2). (B) The insertion times and copy number of clades I (Dasheng) and VII (RIRE2) in SAT are compared. (C) Proportional LTR read depth among the eight species is shown by the colored bars. BAR, O. barthii; GLA, O. glaberrima; GLU, O. glumaepatula; LON, O. longistaminata; LTR, long terminal repeat; MER, O. meridionalis; Mya, million years ago; NIV, O. nivara; OAL, Oryza AA genome of LTR retrotransposons; RUF, O. rufipogon; SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7).

On the whole, LTR retrotransposons are the most plentiful in RUF, resulting in the largest genome size among all AA-genome Oryza species (Figure 1B and Figure S1 and Table S2 in File S1). Different bursts of retrotransposons also contribute to the slightly enlarged genome sizes of SAT and NIV, which grow almost exclusively in Asia. Although not restricted to SAT, this species has accumulated a number of retrotransposons as a result of especially recent amplifications. Besides the above-described patterns observed in OAL001, OAL002, and OAL003, some species-specific bursts were also observed in SAT (OAL007 and OAL011) and MER (OAL012, OAL014, and OAL023). Almost half of the top 44 most abundant retrotransposon families show high proportions of retrotransposon elements in RUF, followed by SAT, NIV, MER, and LON. In spite of their close relationships, we also observe species-specific retrotransposon differences between GLA and its immediate wild progenitor BAR that diverged merely ∼0.26 MYA in Africa (Zhang et al. 2014). It is possible that environmental changes or stochastic mutational processes have induced the species-specific bursts of retrotransposons that previously existed (Grandbastien 1998; Grandbastien et al. 2005). Our findings are similar to O. australiensis, where amplification of only a few LTR retrotransposon families have been sufficient to double its genome size within just a few million years (Piegu et al. 2006).

Conclusions

The evolutionary dynamics and mechanisms of LTR retrotransposon expansion during speciation are largely unknown. Here, we performed a genome-wide comparative analysis of eight AA-genome Oryza species, characterizing a total of 790 LTR retrotransposon families. The resulting evolutionary framework shows that LTR retrotransposons have experienced massive amplifications, albeit with fairly divergent and idiosyncratic life histories since these species diverged ∼4.8 MY. This study provides novel insights into the rapid evolution of rice LTR retrotransposons that shaped the architecture and size of rice genomes during and after their recent speciation.

Supplementary Material

Supplemental material is available online at www.g3journal.org/lookup/suppl/doi:10.1534/g3.116.037572/-/DC1.

Click here for additional data file. (234.4KB, docx)

Acknowledgments

We acknowledge helpful discussions and advice regarding data sources and software from T. Zhu, Y. Liu, Y.L. Liu, Y. Zhang, E.H. Xia, and C. Shi. We are grateful to J.B. Bennetzen for his valuable comments on data analyses. This work was supported by the Project of Innovation Team of Yunnan Province, the Top Talents Program of Yunnan Province (20080A009), the Hundred Oversea Talents Program of Yunnan Province, the Key Project of Natural Science Foundation of Yunnan Province (2010CC011), and the Hundred Talents Program of the Chinese Academy of Sciences (to L.-Z.G.).

Footnotes

Communicating editor: B. J. Andrews

Literature Cited

  1. Aggarwal R. K., Brar D. S., Khush G. S., 1997.  Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Molecular and General Genetics MGG 254: 1–12. [DOI] [PubMed] [Google Scholar]
  2. Baucom R. S., Estill J. C., Chaparro C., Upshaw N., Jogi A., et al. , 2009a Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet. 5: e1000732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baucom R. S., Estill J. C., Leebens-Mack J., Bennetzen J. L., 2009b Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19: 243–254. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bennetzen J. L., 2000.  Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251–269. [PubMed] [Google Scholar]
  5. Bennetzen J. L., 2002.  Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29–36. [DOI] [PubMed] [Google Scholar]
  6. Chen J., Huang Q., Gao D., Wang J., Lang Y., et al. , 2013.  Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat. Commun. 4: 1595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Coffin J. M., Hughes S. H., Varmus H. E., 1997.  Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [PubMed] [Google Scholar]
  8. Cossu R. M., Buti M., Giordani T., Natali L., Cavallini A., 2012.  A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome. Tree Genet. Genomes 8: 61–75. [Google Scholar]
  9. Dolgin E. S., Charlesworth B., 2008.  The effects of recombination rate on the distribution and abundance of transposable elements. Genetics 178: 2169–2177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Du J., Tian Z., Hans C. S., Laten H. M., Cannon S. B., et al. , 2010.  Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J. 63: 584–598. [DOI] [PubMed] [Google Scholar]
  11. Eickbush T. H., Jamburuthugoda V. K., 2008.  The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res. 134: 221–234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Estep M. C., DeBarry J. D., Bennetzen J. L., 2013.  The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity (Edinb) 110: 194–204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Finn R. D., Tate J., Mistry J., Coggill P. C., Sammut S. J., et al. , 2008.  The Pfam protein families database. Nucleic Acids Res. 36: D281–D288. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fu L., Niu B., Zhu Z., Wu S., Li W., 2012.  CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28: 3150–3152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gao L., McCarthy E. M., Ganko E. W., McDonald J. F., 2004.  Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 5: 18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ge S., Sang T., Lu B. R., Hong D. Y., 1999.  Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96: 14400–14405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Grandbastien M.-A., 1998.  Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3: 181–187. [Google Scholar]
  18. Grandbastien M. A., Audeon C., Bonnivard E., Casacuberta J. M., Chalhoub B., et al. , 2005.  Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110: 229–241. [DOI] [PubMed] [Google Scholar]
  19. Hřibová E., Neumann P., Matsumoto T., Roux N., Macas J., et al. , 2010.  Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biol. 10: 204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jiang N., Jordan I. K., Wessler S. R., 2002.  Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. Plant Physiol. 130: 1697–1705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jiang S. Y., Ramachandran S., 2013.  Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum. PLoS One 8: e71118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Jurka J., 1998.  Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8: 333–337. [DOI] [PubMed] [Google Scholar]
  23. Jurka J., 2000.  Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16: 418–420. [DOI] [PubMed] [Google Scholar]
  24. Jurka J., Kapitonov V. V., Pavlicek A., Klonowski P., Kohany O., et al. , 2005.  Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110: 462–467. [DOI] [PubMed] [Google Scholar]
  25. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., et al. , 2007.  Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948. [DOI] [PubMed] [Google Scholar]
  26. Li R., Yu C., Li Y., Lam T. W., Yiu S. M., et al. , 2009.  SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967. [DOI] [PubMed] [Google Scholar]
  27. Li W., Godzik A., 2006.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658–1659. [DOI] [PubMed] [Google Scholar]
  28. Llorens C., Munoz-Pomer A., Bernad L., Botella H., Moya A., 2009.  Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol. Direct 4: 41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Llorens C., Futami R., Covelli L., Dominguez-Escriba L., Viu J. M., et al. , 2011.  The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 39: D70–D74. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ma J., Bennetzen J. L., 2004.  Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101: 12404–12410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ma J., Bennetzen J. L., 2006.  Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc. Natl. Acad. Sci. USA 103: 383–388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ma J., Devos K. M., Bennetzen J. L., 2004.  Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860–869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Matyunina L. V., Bowen N. J., McDonald J. F., 2008.  LTR retrotransposons and the evolution of dosage compensation in Drosophila. BMC Mol. Biol. 9: 55. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. McCarthy E. M., McDonald J. F., 2003.  LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362–367. [DOI] [PubMed] [Google Scholar]
  35. McCarthy E. M., Liu J., Lizhi G., McDonald J. F. 2002.  Long terminal repeat retrotransposons of Oryza sativa. Genome Biol. 3: RESEARCH0053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Ouyang S., Buell C. R., 2004.  The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32: D360–D363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Pereira V., 2004.  Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 5: R79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Petrov D. A., Sangster T. A., Johnston J. S., Hartl D. L., Shaw K. L., 2000.  Evidence for DNA loss as a determinant of genome size. Science 287: 1060–1062. [DOI] [PubMed] [Google Scholar]
  39. Picault N., Chaparro C., Piegu B., Stenger W., Formey D., et al. , 2009.  Identification of an active LTR retrotransposon in rice. Plant J. 58: 754–765. [DOI] [PubMed] [Google Scholar]
  40. Piednoel M., Carrete-Vega G., Renner S. S., 2013.  Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species. Plant J. 75: 699–709. [DOI] [PubMed] [Google Scholar]
  41. Piegu B., Guyot R., Picault N., Roulin A., Sanyal A., et al. , 2006.  Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16: 1262–1269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Roulin A., Piegu B., Fortune P. M., Sabot F., D’Hont A., et al. , 2009.  Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. BMC Evol. Biol. 9: 58. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. SanMiguel P., Gaut B. S., Tikhonov A., Nakajima Y., Bennetzen J. L., 1998.  The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43–45. [DOI] [PubMed] [Google Scholar]
  44. Seberg O., Petersen G., 2009.  A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat. Rev. Genet. 10: 276. [DOI] [PubMed] [Google Scholar]
  45. Smit, A., R. Hubley, and P. Green, 1996–2010 RepeatMasker Open-3.0. Available at: http://www.repeatmasker.org.
  46. Tamura K., Dudley J., Nei M., Kumar S., 2007.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596–1599. [DOI] [PubMed] [Google Scholar]
  47. Tian Z., Rizzon C., Du J., Zhu L., Bennetzen J. L., et al. , 2009.  Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res. 19: 2221–2230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Uozu S., Ikehashi H., Ohmido N., Ohtsubo H., Ohtsubo E., et al. , 1997.  Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol. Biol. 35: 791–799. [DOI] [PubMed] [Google Scholar]
  49. Vaughan D. A., 1989.  The Genus-Oryza L.: Current Status of Taxonomy. IRRI, Manila. [Google Scholar]
  50. Vaughan D. A., Morishima H., Kadowaki K., 2003.  Diversity in the Oryza genus. Curr. Opin. Plant Biol. 6: 139–146. [DOI] [PubMed] [Google Scholar]
  51. Vitte C., Panaud O., 2003.  Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20: 528–540. [DOI] [PubMed] [Google Scholar]
  52. Vitte C., Panaud O., 2005.  LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet. Genome Res. 110: 91–107. [DOI] [PubMed] [Google Scholar]
  53. Vitte C., Panaud O., Quesneville H., 2007.  LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8: 218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Wang H., Liu J. S., 2008.  LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 9: 382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wawrzynski A., Ashfield T., Chen N. W., Mammadov J., Nguyen A., et al. , 2008.  Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol. 148: 1760–1771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wessler S. R., Bureau T. E., White S. E., 1995.  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814–821. [DOI] [PubMed] [Google Scholar]
  57. Wicker T., Keller B., 2007.  Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17: 1072–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wicker T., Sabot F., Hua-Van A., Bennetzen J. L., Capy P., et al. , 2007.  A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8: 973–982. [DOI] [PubMed] [Google Scholar]
  59. Xiong Y., Eickbush T. H., 1990.  Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353–3362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Yang Z., 2007.  PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586–1591. [DOI] [PubMed] [Google Scholar]
  61. Zhang Q. J., Zhu T., Xia E. H., Shi C., Liu Y. L., et al. , 2014.  Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc. Natl. Acad. Sci. USA 111: E4954–E4962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Zhang Y., Liu X. S., Liu Q.-R., Wei L., 2006.  Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 34: 3465–3475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Zhu Q., Ge S., 2005.  Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 167: 249–265. [DOI] [PubMed] [Google Scholar]
  64. Zhu T., Xu P. Z., Liu J. P., Peng S., Mo X. C., et al. , 2014.  Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol. Phylogenet. Evol. 70: 348–361. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Click here for additional data file. (234.4KB, docx)

Data Availability Statement

The authors state that all data necessary for confirming the conclusions presented in the article are represented fully within the article.

Articles from G3: Genes|Genomes|Genetics are provided here courtesy of Oxford University Press

RESOURCES