首页|The haplotype-resolved telomere-to-telomere carnation(Dianthus caryophyllus)genome reveals the correlation between genome architecture and gene expression

The haplotype-resolved telomere-to-telomere carnation(Dianthus caryophyllus)genome reveals the correlation between genome architecture and gene expression

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
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 564479117 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.

Lan Lan、Luhong Leng、Weichao Liu、Yonglin Ren、Wayne Reeve、Xiaopeng Fu、Zhiqiang Wu、Xiaoni Zhang

展开 >

Shenzhen Branch,Guangdong Laboratory of Lingnan Modem 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

College of Science,Health,Engineering and Education,Murdoch University,Murdoch 6150,Western Australia,Australia

Kunpeng Institute of Modern Agriculture at Foshan,Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Agricultural G

Kunpeng 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

Key Laboratory of H

Key Laboratory of Horticultural Plant Biology,College of Horticulture and Forestry Sciences,Huazhong Agricultural University,Wuhan,430070,China

展开 >

国家自然科学基金Shenzhen Fundamental Research ProgramMajor Scientific Research Tasks,Kunpeng Institute of Modern Agriculture at FoshanScientific Research Foundation for the Principal Investigator,Kunpeng Institute of Modern Agriculture at FoshanChinese Academy of Agricultural Sciences Elite Youth ProgramInnovation Program of Chinese Academy of Agricultural Sciences,Science Technology and Innovation Commission of Shenzhen Muni

32002074JCYJ20220818103212025KIMA-ZDKY2022004KIMA-QD2022004110243160001007ZDSYS20200811142605017

2024

10.1093/hr/uhad244

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(1)
  • 93