A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing

Heling Jiang; Xiaoni Zhang; Luhong Leng; Desheng Gong; Xiaohui Zhang; Junyang Liu; Dan Peng; Zhiqiang Wu; Yingxue Yang

doi:10.3389/fpls.2023.1230836

A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing

Front Plant Sci. 2023 Aug 4:14:1230836. doi: 10.3389/fpls.2023.1230836. eCollection 2023.

Authors

Heling Jiang^{1

2}, Xiaoni Zhang¹, Luhong Leng², Desheng Gong², Xiaohui Zhang², Junyang Liu², Dan Peng¹, Zhiqiang Wu^{1

2}, Yingxue Yang^{1

2}

Affiliations

¹ Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China.
² The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Abstract

Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus 'Aili' at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in 'Aili' and previously published 'Francesco' and 'Scarlet Queen'. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.

Keywords: Dianthus caryophyllus; chromosome synteny; genome annotation; genome assembly; phylogenetic analysis.

Associated data

figshare/10.6084/m9.figshare.23808174.v3

Grants and funding

This work was funded by National Natural Science Foundation of China (32002074), Funding of Major Scientific Research Tasks, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-ZDKY2022004 and KIMA-QT2023001), Scientific Research Foundation for Principal Investigator, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-QD2022004), Chinese Academy of Agricultural Sciences Elite Youth Program (110243160001007), Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS 20200811142605017).