LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

Background: LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results: Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion: Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome

Eléments transposables et évolution du génome du riz (genre Oryza)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

LTR retrotransposons in rice (<it>Oryza sativa</it>, L.): recent burst amplifications followed by rapid DNA loss

Abstract Background LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.</p

Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8

International audienc

Editorial: Plant epigenetics and chromatin dynamics - EPIPLANT 2021-2022

International audienc

Draft pan-genome sequence of american B73 and european F2 maize lines

The archive file contains the draft sequence of the american B73 and the european F2 maize lines pan-genome (fast format), the gene prediction for F2-specific regions (gtf format) and the location of F2- and B73-specific regions (gff format). More details are available from README files included in the archive

LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-1

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>sponding to a LTR divergence of 0.01 (0.385 My). For complete copies, ("2 LTRs") this divergence corresponds to the divergence between the two LTRs. For truncated copies (Internal Region [IR], LTR, and LTR-Internal region [LTR-IR]), the divergence is derived from the "2 LTRs" copies (see Materials and Methods and Figure 1)

LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-0

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>proximately at the same time. Upon insertion, all the new copies are identical in sequence as well as the two LTRs of each copy, leading to a null divergence between copies (Div = 0) and between the two LTRs of each copy (Div= 0). Over time, all sequences evolve at the same rate, so both the divergence between two copies and the divergence between the two LTRs of one copy are equal at a given time. Hence, if the nucleotide divergence between a truncated copy and a copy with two LTRs ("2 LTRs" copy) is equal to the nucleotide divergence between the two LTRs of the "2 LTRs" copy, the two copies originated from the same burst of amplification and the insertion date estimated for the "2 LTRs" copy can be used as an approximation of the insertion date of the truncated one

RDA derived Oryza minuta-specific clones to probe genomic conservation across Oryza and introgression into rice (O. sativa L.)

International audienceMolecular markers have been successfully used in rice breeding however available markers based on Oryza sativa sequences are not efficient to monitor alien introgression from distant genomes of Oryza. We developed O. minuta (2n = 48, BBCC)-specific clones comprising of 105 clones (266-715 bp) from the initial library composed of 1,920 clones against O. sativa by representational difference analysis (RDA), a subtractive cloning method and validated through Southern blot hybridization. Chromosomal location of O. minuta-specific clones was identified by hybridization with the genomic DNA of eight monosomic alien additional lines (MAALs). The 37 clones were located either on chromosomes 6, 7, or 12. Different hybridization patterns between O. minuta-specific clones and wild species such as O. punctata, O. officinalis, O. rhizomatis, O. australiensis, and O. ridleyi were observed indicating conservation of the O. minuta fragments across Oryza spp. A highly repetitive clone, OmSC45 hybridized with O. minuta and O. australiensis (EE), and was found in 6,500 and 9,000 copies, respectively, suggesting an independent and exponential amplification of the fragment in both species during the evolution of Oryza. Hybridization of 105 O. minuta specific clones with BB- and CC-genome wild Oryza species resulted in the identification of 4 BB-genome-specific and 14 CC-genome-specific clones. OmSC45 was identified as a fragment of RIRE1, an LTR-retrotransposon. Furthermore this clone was introgressed from O. minuta into the advanced breeding lines of O. sativa