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Article|27 Nov 2023|OPEN
The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression
Lan Lan1,2,3 ,† , Luhong Leng1,3 ,† , Weichao Liu1,3,4 ,† , Yonglin Ren2 , Wayne Reeve2 , , Xiaopeng Fu4 , Zhiqiang Wu1,3 , , Xiaoni Zhang,3 ,
1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
2College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
3Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
4Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
*Corresponding author. E-mail: w.reeve@murdoch.edu.au,wuzhiqiang@caas.cn,zhangxiaoni@caas.cn
Lan Lan,Luhong Leng,Weichao Liu contributed equally to the study.

Horticulture Research 11,
Article number: uhad244 (2024)
doi: https://doi.org/10.1093/hr/uhad244
Views: 20

Received: 26 Jun 2023
Accepted: 12 Nov 2023
Published online: 27 Nov 2023

Abstract

Carnation (Dianthus caryophyllus) is one of the most valuable commercial flowers, due to its richness of color 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 the variety ‘Baltico’, which is the most common white standard variety worldwide. Based on high-depth HiFi, ultra-long nanopore, and Hi-C sequencing data, we assembled the telomere-to-telomere (T2T) genome 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 specific centromere characteristics that cannot be identified by high-order repeats in carnations. We analyzed allele-specific expression in three tissues and the relationship between genome architecture and gene expression in the haplotypes. This demonstrated that the length of the genes, coding sequences, and introns, the exon numbers and the transposable element 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 for functional genomics analysis in further studies and molecular breeding.