Genome-wide comparative analysis of transposable elements in Palmae genomes

Ibrahim, Mohanad A.; Al-Shomrani, Badr M.; Alharbi, Sultan N.; Elliott, Tyler A.; Alsuabeyl, Mohammed S.; Alqahtani, Fahad; Manee, Manee M.

doi:10.52586/5014

Cited by 1 publication

(1 citation statement)

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“…According to a previous analysis, most LTR-RTs identified in Medicago truncatula are relatively recent and were inserted in the last 0.52 MY, with possibly more than 10 million bp lost due to deletion of LTR elements and removal of full-length structures ( Wang and Liu, 2008 ). Ibrahim et al. (2021) examined LTR-RTs in numerous palm genomes and concluded that the Elaeis guineensis genome has undergone several LTR-RT events with different temporal patterns of transposition activity.…”

Section: Resultsmentioning

confidence: 99%

PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons

Mokhtar

Alsamman²,

Allali³

2023

Front. Plant Sci.

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LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia, while the nonautonomous were divided into 224,906 Gypsy, 218,414 Copia, 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. PlantLTRdb is available at https://bioinformatics.um6p.ma/PlantLTRdb.

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Section: Resultsmentioning

confidence: 99%