Developing pangenomes for large and complex plant genomes and their representation formats
Background 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 a comprehensive genomic landscape, revealing both core and accessory genomic elements. T...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/174511 |
| _version_ | 1855525611592744960 |
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| author | Ruperao, P. Rangan, P. Shah, T. Sharma, V. Rathore, A. Mayes, S. Pandey, M.K. |
| author_browse | Mayes, S. Pandey, M.K. Rangan, P. Rathore, A. Ruperao, P. Shah, T. Sharma, V. |
| author_facet | Ruperao, P. Rangan, P. Shah, T. Sharma, V. Rathore, A. Mayes, S. Pandey, M.K. |
| author_sort | Ruperao, P. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
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 a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.
Aim
This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies.
Key scientific concepts of review
Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species’ genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction.
This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity. |
| format | Journal Article |
| id | CGSpace174511 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1745112025-11-11T10:17:39Z Developing pangenomes for large and complex plant genomes and their representation formats Ruperao, P. Rangan, P. Shah, T. Sharma, V. Rathore, A. Mayes, S. Pandey, M.K. graphics haplotype analysis genomes Background 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 a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations. Aim This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies. Key scientific concepts of review Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species’ genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction. This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity. 2025-01 2025-05-09T09:55:11Z 2025-05-09T09:55:11Z Journal Article https://hdl.handle.net/10568/174511 en Open Access application/pdf Elsevier Ruperao, P., Rangan, P., Shah, T., Sharma, V., Rathore, A., Mayes, S. & Pandey, M.K. (2025). Developing pangenomes for large and complex plant genomes and their representation formats. Journal of Advanced Research, 1-18. |
| spellingShingle | graphics haplotype analysis genomes Ruperao, P. Rangan, P. Shah, T. Sharma, V. Rathore, A. Mayes, S. Pandey, M.K. Developing pangenomes for large and complex plant genomes and their representation formats |
| title | Developing pangenomes for large and complex plant genomes and their representation formats |
| title_full | Developing pangenomes for large and complex plant genomes and their representation formats |
| title_fullStr | Developing pangenomes for large and complex plant genomes and their representation formats |
| title_full_unstemmed | Developing pangenomes for large and complex plant genomes and their representation formats |
| title_short | Developing pangenomes for large and complex plant genomes and their representation formats |
| title_sort | developing pangenomes for large and complex plant genomes and their representation formats |
| topic | graphics haplotype analysis genomes |
| url | https://hdl.handle.net/10568/174511 |
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