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Silaiyiman S, Liu J, Wu J, Ouyang L, Cao Z, Shen C. A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes. PLANTS (BASEL, SWITZERLAND) 2025; 14:1399. [PMID: 40364428 PMCID: PMC12073271 DOI: 10.3390/plants14091399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2025] [Revised: 04/27/2025] [Accepted: 05/05/2025] [Indexed: 05/15/2025]
Abstract
Copy number variations (CNVs), as an important structural variant in genomes, are widely present in plants, affecting their phenotype and adaptability. In recent years, CNV research has not only focused on changes in gene copy numbers but has also been linked to complex mechanisms such as genome rearrangements, transposon activity, and environmental adaptation. The advancement in sequencing technologies has made the detection and analysis of CNVs more efficient, not only revealing their crucial roles in plant disease resistance, adaptability, and growth development, but also demonstrating broad application potential in crop improvement, particularly in selective breeding and genomic selection. By studying CNV changes during the domestication process, researchers have gradually recognized the important role of CNVs in plant domestication and evolution. This article reviews the formation mechanisms of CNVs in plants, methods for their detection, their relationship with plant traits, and their applications in crop improvement. It emphasizes future research directions involving the integration of multi-omics to provide new perspectives on the structure and function of plant genomes.
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Affiliation(s)
- Saimire Silaiyiman
- Guangdong Provincial Key Laboratory for Green Agricultural Production and Intelligent Equipment, College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China; (S.S.); (J.L.); (J.W.); (L.O.)
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi 844000, China
| | - Jiaxuan Liu
- Guangdong Provincial Key Laboratory for Green Agricultural Production and Intelligent Equipment, College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China; (S.S.); (J.L.); (J.W.); (L.O.)
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi 844000, China
| | - Jiaxin Wu
- Guangdong Provincial Key Laboratory for Green Agricultural Production and Intelligent Equipment, College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China; (S.S.); (J.L.); (J.W.); (L.O.)
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi 844000, China
| | - Lejun Ouyang
- Guangdong Provincial Key Laboratory for Green Agricultural Production and Intelligent Equipment, College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China; (S.S.); (J.L.); (J.W.); (L.O.)
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Zheng Cao
- Maoming Agricultural Science and Technology Extension Center, Maoming 525000, China;
| | - Chao Shen
- Guangdong Provincial Key Laboratory for Green Agricultural Production and Intelligent Equipment, College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China; (S.S.); (J.L.); (J.W.); (L.O.)
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Cabello-Aguilar S, Vendrell JA, Solassol J. A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology. Curr Issues Mol Biol 2023; 45:9737-9752. [PMID: 38132454 PMCID: PMC10741970 DOI: 10.3390/cimb45120608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Next-generation sequencing (NGS) has taken on major importance in clinical oncology practice. With the advent of targeted therapies capable of effectively targeting specific genomic alterations in cancer patients, the development of bioinformatics processes has become crucial. Thus, bioinformatics pipelines play an essential role not only in the detection and in identification of molecular alterations obtained from NGS data but also in the analysis and interpretation of variants, making it possible to transform raw sequencing data into meaningful and clinically useful information. In this review, we aim to examine the multiple steps of a bioinformatics pipeline as used in current clinical practice, and we also provide an updated list of the necessary bioinformatics tools. This resource is intended to assist researchers and clinicians in their genetic data analyses, improving the precision and efficiency of these processes in clinical research and patient care.
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Affiliation(s)
- Simon Cabello-Aguilar
- Montpellier BioInformatics for Clinical Diagnosis (MOBIDIC), Molecular Medicine and Genomics Platform (PMMG), CHU Montpellier, 34295 Montpellier, France
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Julie A. Vendrell
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Jérôme Solassol
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
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