Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution DOI Creative Commons
Xin Liu, Yan Huang, Sunil Kumar Sahu

et al.

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

Published: Nov. 28, 2024

Abstract Transposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis TEs across 558 high-quality genomes, encompassing 352 species from 221 genera five phyla, ranging algae to angiosperms. We identified over 460 million and 67 transposase domains, systematically assessing impact on host genomes through gene domestication, noncoding RNA generation, duplication. Our revealed 1,258,230 genes domesticated TEs, 1,165,059 ncRNAs originating 10,488,967 TE-induced duplications. These affect more than 2,805 function families, likely planning crucial roles at key stages evolution. Using machine learning-based framework, we uncovered 1,536 lineage-specific families significantly influenced by with enzymes transcription factors being predominant. Notably, elucidated the role expanding factor facilitating potential horizontal transfer synthase families. provides unprecedented insights into TE-driven demonstrating how contributes innovations various evolutionary stages. finding not only enhance understanding dynamics but also offer valuable resources for crop improvement synthetic biology, illumination both current knowledge future processes.

Language: Английский

Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies DOI Creative Commons
Yan Huang, Sunil Kumar Sahu, Xin Liu

et al.

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Summary Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within among species, as well the roles host genes non‐coding RNAs in transposition process, remain elusive. With advancements large‐scale pan‐genome sequencing development open data sharing, comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations identified active TEs 310 plant assemblies across 119 species seven crop populations. Using 811 high‐quality genomes, detected 13 844 553 TE‐induced structural variants (TE‐SVs), providing unprecedented resolution delineating activities. Our integrative analysis revealed a mutual evolutionary relationship between genomes. On one hand, ncRNAs involved evidenced by colocalization coactivation with TEs, may play role chromatin regulation. other drive genetic innovation promoting duplication inserting into regulatory regions. Moreover, influenced linked to growth, nutrient absorption, storage metabolism environmental adaptation, aiding domestication adaptation. This atlas not only reveals functional features activity but also highlights paving way for future exploration TE‐mediated evolution improvement strategies.

Language: Английский

Citations

2
Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa) DOI Creative Commons

Kaitlyn Vondracek,

Fredy Altpeter, Tie Liu

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: April 19, 2024

The cultivated strawberry, Fragaria ×ananassa , is a recently domesticated fruit species of economic interest worldwide. As such, there significant in continuous varietal improvement. Genomics-assisted improvement, including the use DNA markers and genomic selection have facilitated improvements numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations precision nucleotide substitutions target genome, revolutionizing functional genomics crop Genome beginning to gain traction more challenging polyploid crops, allo-octoploid strawberry. release high-quality reference genomes comprehensive subgenome-specific genotyping gene expression profiling data octoploid will lead surge trait discovery modification by using CRISPR/Cas. has already been successfully applied for several genes, anthocyanin content, firmness tolerance post-harvest disease. However, reports on many other important breeding characteristics associated with quality production are still lacking, indicating need streamlined approaches tools . In this review, we present an overview latest advancements knowledge efforts involving CRISPR/Cas enhancement varieties. Furthermore, explore potential applications technology improving Rosaceous plant species.

Language: Английский

Citations

4
Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera DOI Creative Commons
Yilei Wu, Fusheng Wang,

Keliang Lyu

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(17), P. 2462 - 2462

Published: Sept. 3, 2024

Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored roles TEs in genomes Citrus Citrus-related genera by constructing a pan-genome TE library from 20 published accessions. Our results revealed an increase content number types compared original annotations, as well decrease unclassified TEs. The average length per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) 64.76% (Citrus gilletiana) genomes, with mean value 56.95%. A significant positive correlation found between genome size both content. Consistent difference whole-genome (39.83 Mb) genera, contained 34.36 Mb more sequences than Analysis estimated insertion time half-life long terminal repeat retrotransposons (LTR-RTs) suggested that removal not primary factor contributing differences among These findings collectively indicate are determinants play major role shaping structures. Principal coordinate analysis (PCoA) Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) identifiers fragmented were predominantly derived ancestral while intact crucial recent evolutionary diversification Citrus. Moreover, presence or absence near AdhE superfamily closely associated bitterness trait species. Overall, study enhances annotation provides valuable data for future genetic breeding agronomic research

Language: Английский

Citations

4
Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry DOI
Ileana Tossolini,

Rocio Tolley,

Julia Llinares-Gómez

et al.

Published: April 22, 2025

Abstract Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, driving evolution. In this study, we generated comprehensive curated TE library for the woodland strawberry (Fragaria vesca) by integrating two bioinformatic pipelines (EDTA DeepTE). Our annotation revealed that TEs account approximately 37% F. vesca genome. Analysis TE-derived inverted repeats (IRs) miniature inverted-repeat transposable (MITEs) demonstrated their association with 24-nt small interfering RNA (siRNA) production differential DNA methylation patterns across tissues, suggesting role epigenetic regulation particularly during fruit ripening. This MITE-mediated regulatory mechanism was confirmed evaluating expression chromatin organization at FvH4_7g18570, which encodes alcohol acyl transferase (FvAAT1). Three MITEs located upstream or downstream FvAAT1 coding sequence were shown to influence epigenetically expression. Furthermore, analyzed 210 re-sequenced accessions from European germplasm collection identify annotate insertion deletion polymorphisms. A principal component analysis (PCA) based on these polymorphisms subpopulation structures reflect geographic origins. genome-wide study (GWAS) uncovered significant associations between specific economically important traits, including aroma-related volatile compounds size. Among them, hAT MITE near FvH4_2g00610 correlated increased levels γ-decalactone, desirable aroma compound strawberries. These findings underscore functional significance as contributors phenotypic diversity through novel functions. By into population-genomic studies, work provides valuable insights development quality traits. It also highlights potential harnessing TE-mediated variation breeding initiatives editing strategies improve quality.

Language: Английский

Citations

0
Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution DOI Creative Commons
Xin Liu, Yan Huang, Sunil Kumar Sahu

et al.

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

Published: Nov. 28, 2024

Abstract Transposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis TEs across 558 high-quality genomes, encompassing 352 species from 221 genera five phyla, ranging algae to angiosperms. We identified over 460 million and 67 transposase domains, systematically assessing impact on host genomes through gene domestication, noncoding RNA generation, duplication. Our revealed 1,258,230 genes domesticated TEs, 1,165,059 ncRNAs originating 10,488,967 TE-induced duplications. These affect more than 2,805 function families, likely planning crucial roles at key stages evolution. Using machine learning-based framework, we uncovered 1,536 lineage-specific families significantly influenced by with enzymes transcription factors being predominant. Notably, elucidated the role expanding factor facilitating potential horizontal transfer synthase families. provides unprecedented insights into TE-driven demonstrating how contributes innovations various evolutionary stages. finding not only enhance understanding dynamics but also offer valuable resources for crop improvement synthetic biology, illumination both current knowledge future processes.

Language: Английский

Citations

0