Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Juanjuan Chen; Xiaojiao Han; Sicheng Ye; Linxiu Liu; Bingbing Yang; Yongqing Cao; Renying Zhuo; Xiaohua Yao

doi:10.3389/fpls.2022.932926

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Front Plant Sci. 2022 Aug 1:13:932926. doi: 10.3389/fpls.2022.932926. eCollection 2022.

Authors

Juanjuan Chen^{1

2

3}, Xiaojiao Han^{1

2}, Sicheng Ye^{1

2}, Linxiu Liu^{1

2}, Bingbing Yang^{1

2}, Yongqing Cao^{1

2}, Renying Zhuo^{1

2}, Xiaohua Yao^{1

2}

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Hangzhou, China.
² Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China.
³ Forestry Faculty, Nanjing Forestry University, Nanjing, China.

Abstract

Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.

Keywords: Camellia oleifera; co-expression network; integration analysis; low phosphorus stress; miRNA.