Files and links (1)
CC BY V4.0, Open Access
Journal article
The haplotype-resolved T2T carnation ( Dianthus caryophyllus ) genome reveal the correlation between genome architecture and gene expression
Horticulture research, Vol.11(1), uhad244
2023
Abstract
Carnation (Dianthus caryophyllus) is one of the most valuable commercial flowers, due to its richness of colour and form, and its excellent storage and vase life. The diverse demands of the market require faster breeding in carnations. A full understanding of carnations is therefore required to guide the direction of breeding. Hence, we assembled the haplotype-resolved gap-free carnation genome of a variety ‘Baltico’ which is the most common white standard variety worldwide. Based on the high-depth HiFi, ultra-long nanopore and Hi-C sequencing data, we assembled the telomere-to-telomere (T2T) genomes to be 564,479,117 and 568,266,215 bp, for the two haplotypes Hap1 and Hap2, respectively. This T2T genome exhibited great improvement in genome assembly and annotation results compared with the former version. The improvements were seen when different approaches to evaluation were used. Our T2T genome first informs the analysis of the telomere and centromere region, enabling us to speculate about the specific centromere characteristics that cannot be identified by high order repeats in carnations. We analyzed the allele-specific expression in three tissues and the relationship between the genome architecture and gene expression in the haplotypes. This demonstrated that the length of the genes, CDS, introns, the exon numbers and the transposable elements insertions correlate with gene expression ratios and levels. The insertions of transposable elements repress expression in gene regulatory networks in carnation. This gap-free finished T2T carnation genome provides a valuable resource to illustrate the genome characteristics and functional genomics analysis for further studies and molecular breeding.
Details
- Title
- The haplotype-resolved T2T carnation ( Dianthus caryophyllus ) genome reveal the correlation between genome architecture and gene expression
- Authors/Creators
- Lan Lan - Agricultural Genomics Institute at ShenzhenLuhong LengWeichao Liu - Agricultural Genomics Institute at ShenzhenYonglin Ren - Murdoch UniversityWayne Reeve - Murdoch UniversityXiaopeng Fu - Huazhong Agricultural UniversityZhiqiang Wu - Agricultural Genomics Institute at ShenzhenXiaoni Zhang - Agricultural Genomics Institute at Shenzhen
- Publication Details
- Horticulture research, Vol.11(1), uhad244
- Publisher
- Oxford University Press on behalf of Nanjing Agricultural University.
- Identifiers
- 991005622569607891
- Copyright
- © The Author(s) 2024.
- Murdoch Affiliation
- Centre for Sustainable Farming Systems; Centre for Biosecurity and One Health
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Metrics
70 File views/ downloads
168 Record Views