Structural Variation and Its Roles in Plant Genomes

Pan-genome analysis reveals structural variation- associated expression and evolutionary diversity of the ZmCYP450 gene family in maize

A comprehensive pan-genomic view of structural variation, evolutionary patterns, and expression regulation in the ZmCYP450 family is provided, offering a foundation for future functional studies and maize trait improvement.

Pangenome Graph Reveals the Structural Variation Landscape in 2929 Cattle Samples and Its Impact on Gene Regulation.

Structural variations (SVs) represent a significant source of genomic diversity, with demonstrated roles in livestock gene expression and traits. However, a comprehensive understanding of the SV landscape across large sample sets and its impact on gene regulation in cattle remains incomplete. This study aimed to construct high-fidelity pangenome graphs by integrating both assembly-based and whole-genome sequencing (WGS) derived SV catalogs. We evaluated the efficacy of pangenome graphs for SV genotyping and identified 80,328 high-quality SVs from a cohort of 2929 samples. We systematically characterized these SVs, including their linkage disequilibrium with single nucleotide polymorphisms (SNPs), functional annotations, formation mechanisms, and genomic distributions. Furthermore, we generated paired WGS (24.4 ×) and blood RNA-seq data in 170 Simmental cattle. Utilizing our pangenome graphs, we identified 637 SV-expression quantitative trait loci (SV-eQTL), which accounted for 10.81% of expression heritability of target genes, with 38.09% of the effects linked to promoter/enhancer regions. Forty-six of these SV-eQTL were replicated using CattleGTEx results through SV imputation using a joint SNP-SV reference panel. Notably, insertions in the GHSR gene were significantly associated with its expression levels, likely linked to Bos indicus cattle adaptation to heat tolerance. Our findings provide novel insights into the SV landscape and its contribution to gene regulation, underscoring its importance in cattle genetics and genomics.

Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease

Transposable elements (TEs) account for nearly half of the human genome and shape chromatin organization, gene regulation, and genome evolution. However, their contributions to human physiology and disease remain incompletely understood. The most active elements in humans, LINE-1 (L1), Alu, and SVA, retain some copies with the ability to evade epigenetic repression and mobilize via target-primed reverse transcription (TPRT), whereas copies become inactive through various fragmentations and mutations. TE activity contributes to genomic instability and has been implicated in aging, cancer, neurological disorders, chromatin organization, and epigenetic regulation. Studying TE is challenging due to their repetitive and polymorphic nature. Recent advances in sequencing technologies and short- and long-read sequencing platforms, combined with specialized bioinformatic pipelines, currently enable more comprehensive characterization of TE insertions, deletions, expression, and epigenetic status. Computational approaches vary in sensitivity, specificity, and resource requirements, and their performance is influenced by sequencing modality, coverage, and the reference genome used. Assembly-based and read-based methods, as well as integrating methylation data or single-cell data, provide complementary insights into TE biology. This review summarizes the biology of active human TE, surveys state-of-the-art short- and long-read pipelines for TE analysis, and highlights their applications in studies of aging, cancer, and other complex diseases. We also provide practical guidance for selecting appropriate sequencing strategies and tools for TE-focused projects, and discuss emerging approaches and open questions in the field.

Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function

Structural variants (SVs) are abundant in plant genomes and influence agronomic traits, yet their regulatory interpretation remains challenging. Here, we combine pangenome-wide profiling of DNA methylation and chromatin accessibility across 20 barley genotypes, complemented by histone modification and chromatin interaction data in a subset of 10 genotypes. Comparative analysis of genotype-specific epigenomes reveals a globally conserved DNA methylation landscape across the barley pangenome alongside extensive regulatory variability at orthologous genes. We show that SVs do not broadly remodel global chromatin landscapes but instead act through context-dependent rewiring of local regulatory interactions. Despite this epigenomic stability, SVs may contribute to gene expression changes via chromatin contacts. Tissue-specific chromatin accessibility demonstrates that SV effects depend on developmental context. Integrating chromatin state variation with SVs at key vernalization genes explains epigenetic contributions to growth habit diversity. Together, these results provide a framework for interpreting the regulatory consequences of structural variation in crop genomes.

Pan-Genomics in Fruit Crops: Current Progress, Challenges and Future Directions

This review synthesizes the concepts, methodological advances, computational tools, and recent progress in plant pan-genomics, with a focused emphasis on tropical and subtropical fruit crops.

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates