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. 2023 Nov 18;24(1):692.
doi: 10.1186/s12864-023-09786-4.

Genome-wide characterization of regulator of chromosome condensation 1 (RCC1) gene family in Artemisia annua L. revealed a conservation evolutionary pattern

Jieting Chen #  1 , Wenguang Wu #  2 , Xiaoxia Ding  1 , Danchun Zhang  1 , Chunyan Dai  1 , Hengyu Pan  1 , Peiqi Shi  1 , Chanjuan Wu  3 , Jun Zhang  3 , Jianmin Zhao  3 , Baosheng Liao  4 , Xiaohui Qiu  5 , Zhihai Huang  6
Affiliations

Genome-wide characterization of regulator of chromosome condensation 1 (RCC1) gene family in Artemisia annua L. revealed a conservation evolutionary pattern

Jieting Chen et al. BMC Genomics. .

Abstract

Background: Artemisia annua is the major source for artemisinin production. The artemisinin content in A. annua is affected by different types of light especially the UV light. UVR8, a member of RCC1 gene family was found to be the UV-B receptor in plants. The gene structures, evolutionary history and expression profile of UVR8 or RCC1 genes remain undiscovered in A. annua.

Results: Twenty-two RCC1 genes (AaRCC1) were identified in each haplotype genome of two diploid strains of A. annua, LQ-9 and HAN1. Varied gene structures and sequences among paralogs were observed. The divergence of most RCC1 genes occurred at 46.7 - 51 MYA which overlapped with species divergence of core Asteraceae during the Eocene, while no recent novel RCC1 members were found in A. annua genome. The number of RCC1 genes remained stable among eudicots and RCC1 genes underwent purifying selection. The expression profile of AaRCC1 is analogous to that of Arabidopsis thaliana (AtRCC1) when responding to environmental stress.

Conclusions: This study provided a comprehensive characterization of the AaRCC1 gene family and suggested that RCC1 genes were conserved in gene number, structures, constitution of amino acids and expression profiles among eudicots.

Keywords: Artemisia annua; Purifying selection; RCC1; UV-B; UVR8.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Characteristics of AaRCC1 genes. A Phylogenetic relationships (numbers on the nodes represent supporting values). B Gene structures. Blue rectangles represent the coding sequences, thin blue lines connecting two exons represent introns, and thick blue lines represent 5′-UTR or 3′-UTR. C Domain information identified by PfamScan. D Identity and Ka/Ks values between alleles
Fig. 2
Fig. 2
The feature of RCC1 family in five species. A The syntenic relationship of A. annua and H. annuus, green lines represent syntenic RCC1 gene pairs (LQ-9 haplotype 0), the red line indicates  the UVR8 gene pair, while the grey background represents other syntenic gene pairs. B The codon usage ratio of RCC1 orthologs in five species. C The multiple protein sequence alignment of UVR8 in 5 species. D The distribution of Ks value of RCC1 family members in five species
Fig. 3
Fig. 3
The expression patterns of AaRCC1 genes. A The expression profile of 22 AaRCC1 genes in four tissues of two strains. B The expression profile of 22 AaRCC1 genes under different treatments. GA, gibberellin; BR, brassinolide; B, blue light; R, red light; FR, far red light; WL, white light; D, dark; UV_B, UV-B radiation
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