杜仲ARF基因家族全基因组鉴定和表达分析

Objective: Eucommia ulmoides is a traditional medicinal and rubber woody plant that is endemic to China. It is important to study the genes related to growth and development for breeding. Auxin response factor(ARF) is an important transcription factor in the auxin signaling pathways. Study of the role of ARF in E. ulmoides organ development has great values both in theory and practice. Method: Identification of putative EuARF genes from genome data and bio-informatics analysis were performed. The phylogenetic tree was generated using a multiple sequence alignment of the EuARF, AtARF (Arabidopsis thaliana ARF), OsARF (Oryza sativa ARF) and PeARF (Populus × euramericana ARF) proteins. RNA-seq data were used to analyze EuARFs expression profiles. qRT-PCR were used to analyze the expression patterns of these genes and miRNAs in organs at different developmental stages. Result: A total of 18 EuARFs were identified in the E. ulmoides genome. These EuARFs were divided into five classes by phylogenetic tree and predicted that eu-miR160s target EuARFs of class Ⅱ and eu-miR167s target EuARFs of class Ⅴ except EuARF8.2. The expression patterns showed that the expression of EuARFs in different growth stages of leaves was different, and the expression of EuARFs in class Ⅴ and EuARF19.2 in class Ⅵ were higher in 3 cm long growing leaves and unfolded young leaves. The qRT-PCR indicated that EuARFs expressed in organs (leaf, root and stem) at different developmental stages (young and mature). In addition, EuARFs were up-regulated in mature roots and down-regulated in mature leaves and stems. Meanwhile eu-miR160s was mainly expressed in young roots, and eu-miR167s was mainly expressed in mature leaves. Conclusion: A total of 18 EuARFs were identified in the genome of E. ulmoides. These EuARFs were expressed in organs (roots, stems and leaves) at different developmental stages (young and mature) under normal growth conditions. The expression level indicates that EuARFs in class V has a regulating role for seedlings growth and development and EuARF19.2 plays an important role in regulating the leaf growth.