Characterization and comparative profiling of the small RNA transcriptomes in two phases of flowering in Cymbidium ensifolium

BMC Genomics

Research Article

Guoqiang Jin¹  Feng Jin²  Dianxing Wu³  Xiaoli Shu³  Xiang Ma⁴  Aaron Jackson⁵  Liang Jin⁶  Xiaobai Li⁷ 

[1] Agricultural Bureau of Yuhang District, Yuhang, Hangzhou, Peoples Republic of China;Hubei University, College of Life Sciences, 430062, Wuhan, People’s Republic of China;International Atomic Energy Agency Collaborating Center, Zhejiang University, 310029, Hangzhou, Peoples Republic of China;Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, People’s Republic of China;USDA-ARS, Dale Bumpers National Rice Research Center, 72160, Stuttgart, Arkansas, USA;Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, 310021, Hangzhou, People’s Republic of China;Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, 310021, Hangzhou, People’s Republic of China;International Atomic Energy Agency Collaborating Center, Zhejiang University, 310029, Hangzhou, Peoples Republic of China;

关键词: Gene Ontology;    Floral Organ;    miRNA Family;    Floral Development;    Auxin Response Factor;   

DOI  :  10.1186/s12864-015-1764-1

 received in 2015-04-13, accepted in 2015-07-10,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundCymbidium ensifolium is one of the most important ornamental flowers in China, with an elegant shape, beautiful appearance, and a fragrant aroma. Its unique flower shape has long attracted scientists. MicroRNAs (miRNAs) are critical regulators in plant development and physiology, including floral development. However, to date, few studies have examined miRNAs in C. ensifolium.ResultsIn this study, we employed Solexa technology to sequence four small RNA libraries from two flowering phases to identify miRNAs related to floral development. We identified 48 mature conserved miRNA and 71 precursors. These conserved miRNA belonged to 20 families. We also identified 45 novel miRNA which includes 21 putative novel miRNAs*, and 28 hairpin forming precursors. Two trans-acting small interfering RNAs (ta-siRNAs) were identified, one of which was homologous to TAS3a1. TAS3a1 belongs to the TAS3 family, which has been previously reported to target auxin response factors (ARF) and be involved in plant growth and floral development. Moreover, we built a C. ensifolium transctriptome database to identify genes targeted by miRNA, which resulted in 790 transcriptomic target unigenes. The target unigenes were annotated with information from the non-redundant (Nr), gene ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto encyclopedia of genes and genomes (KEGG) database. The unigenes included MADS-box transcription factors targeted by miR156, miR172 and miR5179, and various hormone responding factors targeted by miR159. The MADS-box transcription factors are well known to determine the identity of flower organs and hormone responding factors involved in floral development. In expression analysis, three novel and four conserved miRNA were differentially expressed between two phases of flowering. The results were confirmed by RNA-seq and qRT-PCR. The differential expression of two miRNA, miR160 and miR396, targeted ARFs and growth regulating factor (GRF), respectively. However, most of these small RNA were clustered in the uncharacterized group, which suggests there may be many novel small non-coding RNAs yet to be discovered.ConclusionOur study provides a diverse set of miRNAs related to cymbidium floral development and serves as a useful resource for investigating miRNA-mediated regulatory mechanisms of floral development.

【 授权许可】

CC BY   
© Li et al. 2015