The haplotype-resolved T2T carnation (Dianthus caryophyllus) genome reveal the correlation between genome architecture and gene expression

November 2023

Lan Lan, Luhong Leng, Weichao, Yonglin Ren, Wayne Reeve, Xiaopeng Fu, Zhiqiang Wu, Xiaoni Zhang
“Carnation (Dianthus caryophyllus) is one of the most valuable commercial 45 flowers, due to its richness of colour and form, and its excellent storage and vase life. 46 The diverse demands of the market require faster breeding in carnations. A full 47 understanding of carnations is therefore required to guide the direction of breeding. 48 Hence, we assembled the haplotype-resolved gap-free carnation genome of a variety 49 ‘Baltico’ which is the most common white standard variety worldwide. Based on the 50 high-depth HiFi, ultra-long nanopore and Hi-C sequencing data, we assembled the 51 telomere-to-telomere (T2T) genomes to be 564,479,117 and 568,266,215 bp, for the 52 two haplotypes Hap1 and Hap2, respectively. This T2T genome exhibited great 53 improvement in genome assembly and annotation results compared with the former 54 version. The improvements were seen when different approaches to evaluation were 55 used. Our T2T genome first informs the analysis of the telomere and centromere 56 region, enabling us to speculate about the specific centromere characteristics that 57 cannot be identified by high order repeats in carnations. We analyzed the allele-58 specific expression in three tissues and the relationship between the genome 59 architecture and gene expression in the haplotypes. This demonstrated that the length 60 of the genes, CDS, introns, the exon numbers and the transposable elements insertions 61 correlate with gene expression ratios and levels. The insertions of transposable 62 elements repress expression in gene regulatory networks in carnation. This gap-free 63 finished T2T carnation genome provides a valuable resource to illustrate the genome 64 characteristics and functional genomics analysis for further studies and molecular 65 breeding. “

Sage Science Products:
The SageHLS instrument was used to size select Ultra High Molecular Weight DNA for Oxford Nanopore Promethion sequencing (Genome Center of Grandomics, Wuhan China)

Author Affiliations:

Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, China

College of Science, Health, Engineering and Education, Murdoch University, Western Australia

Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, China

Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China

Preprint – Horticulture Research
DOI: 10.1093/hr/uhad244

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