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

Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(4)

Published: Feb. 1, 2025

SUMMARY Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects on yields, we need develop varieties that tolerant water‐limited conditions. We aimed determine how diverse types (winter/spring oilseed, tuberous, leafy) allopolyploid Brassica napus , species contains economically important rapeseed oilseed crop, respond prolonged water limitation. exposed plants an 80% reduction in assessed growth color high‐throughput phenotyping system over 4 weeks ended experiment with tissue collection for time course transcriptomic study. found overall across cultivars but varying degrees. Diel transcriptome analyses revealed significant accession‐specific changes time‐of‐day regulation photosynthesis, carbohydrate metabolism, sulfur metabolism. Interestingly, there was extensive variation which homoeologs two parental subgenomes responded limitation could be due differences regulatory regions these lines. Follow‐up experiments select confirmed maintained photosynthetic health during while slowing growth. In examined, day levels glucosinolates, sulfur‐ nitrogen ‐rich specialized metabolites, consistent diel responses. These results suggest lines adjusting their stores under conditions through distinct regulation.

Language: Английский