Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

Mobile DNA, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 12, 2025

Abstract Background LTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers genome evolution. Most LTR-RT copies in defective elements found as truncated copies, nested insertions or part more complex structures. The recent availability highly contiguous assemblies based on long-read sequences now allows to perform detailed characterization these structures evaluate their importance for Results analysis two rice loci containing showed that they consist tandem arrays LTR sharing internal LTRs. Our analyses suggests tandems the result single insertion not recombination independent elements. results also suggest gypsy may be prone form We show polymorphic therefore have potential generate genetic variability. developed computational pipeline (IDENTAM) scans identifies candidates. Using this tool, we detected 266 pangenome built from 76 accessions cultivated wild rice, showing frequent rice. Running IDENTAM Arabidopsis, almond cotton different size, complexity ploidy level. differentiating intra-element variations at nucleotide level among haplotypes is very high, graph-based pangenomic methodologies appropriate resolve Conclusions can arrays. These relatively abundant widespread kingdom. Future studies will contribute understanding how originate whether variability has functional impact.

Language: Английский

---

The Combination of Start-Codon-Targeted (SCoT) and Falling Stone (FaSt) Transposon-Specific Primers Provides an Efficient Marker Strategy for Prunus Species

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(9), P. 3972 - 3972

Published: April 23, 2025

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus species and 28 of European plum. Compared SCoT-only analyses, SCoT–FaSt combination produced fewer total bands but a higher percentage polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, Shannon’s index. markers generated across broader size range, which made gel patterns less dense, enabling more accurate detection differentially amplified fragments. Neighbor-joining principal component analyses confirmed that provided sufficient phylogenetic resolution at both interspecific intraspecific levels. The sequencing 32 amplicons revealed FaSt elements 26 fragments, SCoT preferentially annealing GC-rich exonic intergenic regions. Seventeen protein-coding one RNA-coding were partially identified, localized UTRs introns genes key physiological functions. Comparative analysis indicated biased distribution between Cerasus subgenera. In silico findings suggest are fragmented cherry species, potentially contributing subgeneric divergence. Overall, marker system is effective evaluating reconstructing relationships, elucidating genomic impact an active Mutator-like transposon.

Language: Английский

---

Mapping the genomic landscape of Prunus spp. with PrunusMap

Horticulture Research, Journal Year: 2024, Volume and Issue: 12(2)

Published: Oct. 24, 2024

Language: Английский

---

QTL mapping of almond kernel quality traits in the F1 progeny of ‘Marcona’ × ‘Marinada’

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 27, 2024

Almond breeding is increasingly focusing on kernel quality. However, unlike other agronomic traits, the genetic basis of physical and chemical quality traits has been poorly investigated. To address this gap, we conducted a QTL mapping these to enhance our understanding their control. We phenotyped fruit samples from an F

Language: Английский

---

Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 4, 2024

Background LTR-retrotransposons (LTR-RT) are a major component of plant genomes and driver genome evolution. Most LTR-RT copies in defective elements, found as truncated copies, nested insertions or being part more complex structures. With the availability highly contiguous assemblies based on long-read sequences it has become feasible detailed characterization these structures evaluation their importance for Results The analysis two rice loci containing showed that they consist tandem arrays LTR sharing internal LTRs. Our show tandems not result single insertion recombination independent elements. results suggest gypsy elements may be prone to form We polymorphic have therefore potential generate genetic phenotypic variability. developed computational pipeline, IDENTAM, scans identifies candidates detected 307 pangenome built from 75 accessions cultivated wild rice, showing frequent species. Running IDENTAM Arabidopsis, almond cotton different size, complexity ploidy levels. differentiating intra-element variations at nucleotide level among haplotypes is very high, we graph-based pangenomic methodologies appropriate resolve Conclusions LTR-RTs can These relatively abundant widespread kingdom. Future studies will contribute understand how originate if variability functional impact.

Language: Английский

---

Genetic mapping reveals a major locus for red leaf blotch tolerance in almond

Scientia Horticulturae, Journal Year: 2024, Volume and Issue: 339, P. 113901 - 113901

Published: Dec. 17, 2024

Language: Английский

---