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

Abstract

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.

A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index

“…4 ). Many previous studies have characterized LTR-RTs of Solanaceae family species such as Capsicum annuum ( de Assis et al 2020 ; Mokhtar et al 2023 ), Solanum melongena ( Barchi et al 2019 ), Datura stramonium ( De-la-Cruz et al 2021 ) and Solanum lycopersicum ( Paz et al 2017 ; Mokhtar et al 2023 ). In a recent study, the LAI method was used to verify the quality of de novo assembly of the genomes of wild tomatoes Solanum pimpinellifolium and Solanum lycopersicum var.…”

“…In some genomes, TE content ranges from 3 % to over 85 % and the genome size is positively correlated with the TE content ( Kress et al 2022 ). LTR-RTs are a class of TE scattered throughout most plant genomes and range in size from 4 to 20 kb (Mokhtar et al 2021a , 2023 ). Intact LTR-RT elements in the final plant genome assemblies yielded more intact elements than in the draft genomes, supporting the use of LAI as a measure of genome sequence quality and completeness ( Ou et al 2018 ).…”

Transposable elements: multifunctional players in the plant genome

“…TE insertions within genes can inactivate them or alter their splicing patterns, leading to new proteins ( Muñoz-López and García-Pérez, 2010 ). The insertion of TEs near genes can lead to new control mechanisms and influence gene expression and function ( Chuong et al., 2017 ; Mokhtar et al., 2023 ). For example, the retrotransposon Gret1 upstream of a gene that regulates anthocyanin biosynthesis in grapes causes a white color phenotype, while the presence of a solo-LTR at the insertion site can partially convert the white berry phenotype to a red color ( Azuma and Kobayashi, 2022 ) and retrotransposon insertion into a MADS-box gene in primrose flowers alters the “tube-in-tube” phenotype ( Li et al., 2014 ).…”

“…On the other hand, the non-autonomous LTR-RTs, are the elements that lack one or more of the protein-coding domains required for mobilization. The complete structure of LTR-RT consists of two identical LTRs surrounded by TSDs of typically 4-6 base pairs (bp), a PBS (primer binding site), a PPT (polypurine tract), a Gag gene encoding a polyprotein, and a Pol gene ( Mokhtar et al., 2023 ). The Pol gene encodes domains such as reverse transcriptase (RT), RH (RNase H), IN (integrase), and PR (protease).…”

MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes

“…Once LTR-RTs are identified, they can be annotated using various databases and resources. Some examples of databases and resources developed for this purpose are TREP ( Wicker et al., 2002 ), RepBase ( Jurka et al., 2005 ), REXdb ( Neumann et al., 2019 ), PlantRep ( Amselem et al., 2019 ), and PlantLTRdb ( Mokhtar et al., 2023b ). These tools and databases have been used to create automatized pipelines for LTR-RT analysis, including REPCLASS ( Feschotte et al., 2009 ), EDTA ( Ou et al., 2019 ), and Inpactor2 ( Orozco-Arias et al., 2022 ).…”