Developing pangenomes for large and complex plant genomes and their representation formats

Journal of Advanced Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct comprehensive landscape, revealing both core and accessory elements. This approach enables identification novel genes, structural variations, gene presence-absence providing insights into species evolution, adaptation, trait variation. Representing requires innovative visualization formats that effectively convey complex structures variations. review delves contemporary methodologies recent advancements in constructing pangenomes, particularly plant genomes. It examines structure pangenome representation, including format comparison, conversion, techniques, their implications for enhancing crop improvement strategies. Earlier comparative have illuminated sequences, copy number variations across diverse concept pan-genome, which captures broad spectrum genotypes, offers holistic perspective species' makeup. However, pan-genome plants with larger genomes poses challenges, managing vast genome sequence comprehending germplasm. To address these researchers explored cost-effective alternatives encapsulate single known as pangenome. involves reducing volume sequences while focusing on With growing prominence genomics, several software tools emerged facilitate construction. sheds light developing utilizing tailored pan-genomes plants. also discusses representation suitable downstream analyses, offering valuable landscape evolutionary dynamics In summary, this underscores significance construction resolving architecture plants, those provides overview advancements, aiding exploring understanding diversity.

Language: Английский

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Comprehensive Analysis of Ghd7 Variations Using Pan-Genomics and Prime Editing in Rice

Genes, Journal Year: 2025, Volume and Issue: 16(4), P. 462 - 462

Published: April 17, 2025

The Ghd7 gene in rice plays a crucial role determining heading date, plant height, and grain yield. However, the variations their functional implications across different accessions are not fully understood. Based on release of large amount genome data recent years, we investigated through pan-genome analysis 372 diverse varieties figured out structural (SVs) locus. due to high cost pan-genomes, most genomes based next-generation sequencing (NGS) now. Therefore, developed method for identifying SVs using NGS Polymerase Chain Reaction (PCR) results identified 977 carrying such Ghd7. Furthermore, 46 single-nucleotide polymorphisms (SNPs) one insertion-deletion (InDel) coding region They classified into 49 haplotypes. Notably, splice-site mutation haplotype H6 causes aberrant mRNA splicing. Using prime editing (PE) technology, successfully restored Yixiang 1B (YX1B), delaying date by approximately 16 days. This modification synchronized between YX1B restorer line Yahui 2115 (YH2115R), enhancing hybrid seed production efficiency. In conclusion, our findings highlight potential integrating pan-genomics precision accelerate crop improvement enhance agronomic traits.

Language: Английский

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Genomic research and genetic improvement of orphan crops: novel strategies for addressing global food security challenges

Published: Jan. 1, 2025

Language: Английский

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