title: Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis.
abstract: BACKGROUND
  Small RNA (sRNA) play pivotal roles in reproductive development, and their biogenesis and action mechanisms are well characterised in angiosperm plants; however, corresponding studies in conifers are very limited. To improve our understanding of the roles of sRNA pathways in the reproductive development of conifers, the genes associated with sRNA biogenesis and action pathways were identified and analysed, and sRNA sequencing and parallel analysis of RNA ends (PARE) were performed in male and female cones of the Chinese pine (Pinus tabuliformis).
  
  
  RESULTS
  Based on high-quality reference transcriptomic sequences, 21 high-confidence homologues involved in sRNA biogenesis and action in P. tabuliformis were identified, including two different DCL3 genes and one AGO4 gene. More than 75 % of genes involved in sRNA biogenesis and action have higher expression levels in female than in male cones. Twenty-six microRNA (miRNA) families and 74 targets, including 46 24-nt sRNAs with a 5' A, which are specifically expressed in male cones or female cones and probably bind to AGO4, were identified.
  
  
  CONCLUSIONS
  The sRNA pathways have higher activity in female than in male cones, and the miRNA pathways are the main sRNA pathways in P. tabuliformis. The low level of 24-nt short-interfering RNAs in conifers is not caused by the absence of biogenesis-related genes or AGO-binding proteins, but most likely caused by the low accumulation of these key components. The identification of sRNAs and their targets, as well as genes associated with sRNA biogenesis and action, will provide a good starting point for investigations into the roles of sRNA pathways in cone development in conifers.
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. arrennew@bjfu.edu.cn.
authors.forename: Shi-Hui
authors.initials: SH
authors.lastname: Niu
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. liuliuandmimi@126.com.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. yuanhuwei86@163.com.
authors.forename: Hu-Wei
authors.initials: HW
authors.lastname: Yuan
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. lipei-meinv@163.com.
authors.forename: Pei
authors.initials: P
authors.lastname: Li
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. liyue@bjfu.edu.cn.
authors.forename: Yue
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. bjfuliwei@bjfu.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
mesh_terms: D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D023061:Gene Order; D017343:Genes, Plant; D010802:Phylogeny; D028223:Pinus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D012098:Reproduction / Q000235:genetics; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D058727:RNA, Small Untranslated