title: Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs in Camellia during floral organ development.
abstract: In plants, miRNAs are endogenous small RNAs derived from single-stranded precursors with hairpin structures. The evolution of miRNAs and their targets represents one of the most dynamic circuits directing gene expression, which may play fundamental roles in shaping the development of distinct plant organs. Here we performed high-throughput small RNA sequencing in five organ types of Camellia azalea to capture the spatial profile of small non-coding RNA. In total we obtained >227 million high-quality reads and identified 175 miRNAs with mature and precursor sequences. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as 'newly evolved' miRNA genes. Twelve miRNAs were identified to be specific in the genus Camellia, supporting the lineage-specific manner of expansion of 'young' miRNAs. Through differential expression analysis, we showed that many miRNAs were preferentially abundant in certain organ types. Moreover, hierarchical clustering analysis revealed distinctive expression patterns of tissue-specific miRNAs. Gene Ontology enrichment analysis of targets of stamen- and carpel-specific miRNA subclusters showed that miRNA-target regulatory circuits were involved in many important biological processes, enabling their proper specification and organogenesis, such as 'DNA integration' and 'fruit development'. Further, quantitative PCR of key miRNAs and their target genes revealed anti-correlated patterns, and uncovered the functions of key miRNA-target pairs in different floral organs. Taken together, this work yielded valuable information on miRNA-target regulation in the control of floral organ development and sheds light on the evolution of lineage-specific miRNAs in Camellia.
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China Key Laboratory of Forest genetics and breeding, Zhejiang Province 311400, China hfyin@sibs.ac.cn jiyuan_li@126.com.
authors.forename: Hengfu
authors.initials: H
authors.lastname: Yin
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China Key Laboratory of Forest genetics and breeding, Zhejiang Province 311400, China.
authors.forename: Zhengqi
authors.initials: Z
authors.lastname: Fan
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China Key Laboratory of Forest genetics and breeding, Zhejiang Province 311400, China.
authors.forename: Xinlei
authors.initials: X
authors.lastname: Li
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China.
authors.forename: Jiangying
authors.initials: J
authors.lastname: Wang
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China.
authors.forename: Weixin
authors.initials: W
authors.lastname: Liu
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China Key Laboratory of Forest genetics and breeding, Zhejiang Province 311400, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Ying
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors.forename: Zhongchi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China Key Laboratory of Forest genetics and breeding, Zhejiang Province 311400, China hfyin@sibs.ac.cn jiyuan_li@126.com.
authors.forename: Jiyuan
authors.initials: J
authors.lastname: Li
mesh_terms: D028244:Camellia / Q000235:genetics / Q000254:growth & development*; D017124:Conserved Sequence / Q000235:genetics* / Q000502:physiology; D035264:Flowers / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000502:physiology; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs
keywords: Camellia; differential expression; floral development; lineage specific; miRNA–target regulation.; microRNA identification