Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge - A Transcriptomics Perspective

Published: July 4, 2024

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, significant evolutionary process plant kingdom. Transcriptomic analysis provides valuable insights fate duplicated genes, novelties, and environmental adaptations exhibited by allopolyploid plants. However, transcriptome profiling is challenging due to genomic redundancy, which further complicated presence multiple chromosomes sets variations among homoeologs allelic genes. Prior analysis, sub-genome phasing homoeology inference are essential for obtaining comprehensive view gene expression. This review aims clarify terminology this field, identify most aspects explain their inherent difficulties, suggest reliable analytic strategies. Furthermore, bulk RNA-seq highlighted as primary method studying expression, with an emphasis on critical steps read mapping normalization differential expression analysis.

Language: Английский

---

The latest on study and research abroad during mid- and post-COVID-19 periods

Breeding Research, Journal Year: 2024, Volume and Issue: 26(1), P. 85 - 90

Published: June 1, 2024

Language: Английский

---

Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

Genes, Journal Year: 2024, Volume and Issue: 15(8), P. 977 - 977

Published: July 24, 2024

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, significant evolutionary process plant kingdom. Transcriptomic analysis provides invaluable insights allopolyploid by elucidating fate duplicated genes, revealing novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how genes have evolved to acquire new functions regulatory roles. This often leads development novel traits adaptive strategies that leverage thrive diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation genetic complexity underlying allopolyploidy but also underscores importance agriculture ecosystem resilience. However, transcriptome profiling is challenging due genomic redundancy, which further complicated presence multiple chromosomes sets variations among homoeologs allelic genes. Prior analysis, sub-genome phasing homoeology inference are essential for obtaining comprehensive view expression. review aims clarify terminology this field, identify most aspects explain inherent difficulties, suggest reliable analytic strategies. Furthermore, bulk RNA-seq highlighted as primary method studying expression, focusing on critical steps like read mapping normalization differential analysis. approach effectively captures from both genomes, facilitating combined profiles. Its sensitivity detecting low-abundance transcripts allows subtle differences between be identified, crucial understanding dynamics balance allopolyploids.

Language: Английский

---

Wheat: Recent Advances in Genomics to Explore the History of Domestication and Polyploidization

Evolutionary studies, Journal Year: 2024, Volume and Issue: unknown, P. 155 - 180

Published: Jan. 1, 2024

Language: Английский

---