Search for Dispersed Repeats in Oryza sativa Genome Using Iterative Procedure Method
Received date: 2024-12-25
Accepted date: 2025-04-18
Online published: 2025-08-06
Valentina Rudenko, Eugene Korotkov . Search for Dispersed Repeats in Oryza sativa Genome Using Iterative Procedure Method[J]. Rice Science, 2025 , 32(4) : 472 -474 . DOI: 10.1016/j.rsci.2025.04.008
| [1] | Bao W D, Kojima K K, Kohany O. 2015. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA, 6: 11. |
| [2] | Bariah I, Keidar-Friedman D, Kashkush K. 2020. Where the wild things are: Transposable elements as drivers of structural and functional variations in the wheat genome. Front Plant Sci, 11: 585515. |
| [3] | Crooks G E, Hon G, Chandonia J M, et al. 2004. WebLogo: A sequence logo generator. Genome Res, 14(6): 1188-1190. |
| [4] | Durán-Meza G, López-García J, del Río-Correa J L. 2019. The self-similarity properties and multifractal analysis of DNA sequences. Appl Math Nonlinear Sci, 4(1): 267-278. |
| [5] | Flynn J M, Hubley R, Goubert C, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA, 117(17): 9451-9457. |
| [6] | Gu W J, Castoe T A, Hedges D J, et al. 2008. Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem, 380(1): 77-83. |
| [7] | Jeong H H, Yalamanchili H K, Guo C W, et al. 2018. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Pac Symp Biocomput, 23: 168-179. |
| [8] | Kohany O, Gentles A J, Hankus L, et al. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 7: 474. |
| [9] | Korotkov E, Suvorova Y, Kostenko D, et al. 2023. Search for dispersed repeats in bacterial genomes using an iterative procedure. Int J Mol Sci, 24(13): 10964. |
| [10] | Li R Q, Ye J, Li S G, et al. 2005. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol, 1(4): e43. |
| [11] | Nicolas J, Tempel S, Fiston-Lavier A S, et al. 2022. Finding and characterizing repeats in plant genomes. Methods Mol Biol, 2443: 327-385. |
| [12] | Orozco-Arias S, Isaza G, Guyot R. 2019. Retrotransposons in plant genomes: Structure, identification, and classification through bioinformatics and machine learning. Int J Mol Sci, 20(15): 3837. |
| [13] | Rudenko V, Korotkov E. 2024. Study of dispersed repeats in the Cyanidioschyzon merolae genome. Int J Mol Sci, 25(8): 4441. |
| [14] | Schnable P S, Ware D, Fulton R S, et al. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science, 326: 1112-1115. |
| [15] | Storer J, Hubley R, Rosen J, et al. 2021. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA, 12(1): 2. |
| [16] | Storer J M, Hubley R, Rosen J, et al. 2022. Methodologies for the de novo discovery of transposable element families. Genes, 13(4): 709. |
| [17] | Sun X P, Xiang Y L, Dou N N, et al. 2023. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol, 41: 120-127. |
| [18] | Yin C C. 2017. Identification of repeats in DNA sequences using nucleotide distribution uniformity. J Theor Biol, 412: 138-145. |
/
| 〈 |
|
〉 |