Identification of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis

BMC Plant Biology

Research Article

Yi Zheng¹  Zhangjun Fei²  Yanjun He³  Lifei Chen³  Jingli Chen³  Yan Wang³  Gang Lu³  Li Qin³ 

[1] Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, 14853, Ithaca, New York, USA;Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, 14853, Ithaca, New York, USA;USDA Robert W. Holley Center for Agriculture and Health, Tower Road Ithaca, 14853, New York, USA;Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, 310058, Hangzhou, PR China;

关键词: Asparagus officinalis;    miRNAs;    High-throughput sequencing;    Degradome analysis;    Sex determination;   

DOI  :  10.1186/s12870-016-0770-z

 received in 2015-12-01, accepted in 2016-04-06,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (miRNAs), a class of non-coding small RNAs (sRNAs), regulate various biological processes. Although miRNAs have been identified and characterized in several plant species, miRNAs in Asparagus officinalis have not been reported. As a dioecious plant with homomorphic sex chromosomes, asparagus is regarded as an important model system for studying mechanisms of plant sex determination.ResultsTwo independent sRNA libraries from male and female asparagus plants were sequenced with Illumina sequencing, thereby generating 4.13 and 5.88 million final clean reads, respectively. Both libraries predominantly contained 24-nt sRNAs, followed by 21-nt sRNAs. Further analysis identified 154 conserved miRNAs, which belong to 26 families, and 39 novel miRNA candidates seemed to be specific to asparagus. Comparative profiling revealed that 63 miRNAs exhibited significant differential expression between male and female plants, which was confirmed by real-time quantitative PCR analysis. Among them, 37 miRNAs were significantly up-regulated in the female library, whereas the others were preferentially expressed in the male library. Furthermore, 40 target mRNAs representing 44 conserved and seven novel miRNAs were identified in asparagus through high-throughput degradome sequencing. Functional annotation showed that these target mRNAs were involved in a wide range of developmental and metabolic processes.ConclusionsWe identified a large set of conserved and specific miRNAs and compared their expression levels between male and female asparagus plants. Several asparagus miRNAs, which belong to the miR159, miR167, and miR172 families involved in reproductive organ development, were differentially expressed between male and female plants, as well as during flower development. Consistently, several predicted targets of asparagus miRNAs were associated with floral organ development. These findings suggest the potential roles of miRNAs in sex determination and reproductive developmental processes in asparagus.

【 授权许可】

CC BY   
© Chen et al. 2016