Doctoral Thesis
Genomic Insights into Evolution and Genome Architecture of Caryophyllales from High-Quality Floral Genomes
Murdoch University
Doctor of Philosophy (PhD), Murdoch University
2025
DOI:
https://doi.org/10.60867/00000067
Abstract
Bougainvillea and Dianthus are among the most commercially valuable ornamental flowers worldwide. Comparing with traditional breeding, molecular breeding provides an efficient alternative to accelerate breeding and achieve targeted improvements; however, the absence of high-quality reference genomes has limited our understanding of the molecular mechanisms underlying key ornamental traits, thereby constraining breeding innovation.
This thesis presents two chromosome-scale genome assemblies for Bougainvillea and a haplotype-resolved telomere-to-telomere genome assembly for Dianthus, representing significant advances in ornamental plant genomics. Comparative genomic analyses of Bougainvillea reveal extensive ancestral introgression events within Caryophyllales, while multi-omics investigations elucidate the molecular basis of bract colour differentiation. Based on the first T2T Dianthus assembly, this study provides major improvements over previous genome versions, explores the genome-wide relationship between genomic architecture and allele expression, and demonstrates that transposable element insertions can markedly repress gene expression within regulatory networks.
Additionally, this thesis summarizes practical strategies and key considerations for genome assembly and annotation, offering a detailed and systematic overview to enhance the efficiency and quality of these processes. Together, these genomic resources and methodological insights lay a solid foundation for molecular breeding and trait improvement in Bougainvillea and Dianthus, addressing the growing demands of the global floriculture industry.
Details
- Title
- Genomic Insights into Evolution and Genome Architecture of Caryophyllales from High-Quality Floral Genomes
- Authors/Creators
- Lan Lan
- Contributors
- Chengdao Li (Supervisor) - Murdoch University, Centre for Crop and Food InnovationWayne Reeve (Supervisor)Zhiqiang Wu (Supervisor) - Agricultural Genomics Institute at ShenzhenLi Wang (Supervisor) - Agricultural Genomics Institute at Shenzhen
- Awarding Institution
- Murdoch University; Doctor of Philosophy (PhD)
- Publisher
- Murdoch University
- Identifiers
- 991005861093807891
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences; College of Environmental and Life Sciences
- Resource Type
- Doctoral Thesis
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