Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis.

Shi-Hui Niu,Wei Li,Yue Li,Chang Liu,Hu-Wei Yuan,Pei Li

doi:10.1186/s12864-015-1885-6

Abstract

BackgroundSmall 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).ResultsBased 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1885-6) contains supplementary material, which is available to authorized users.

Highlights

Small RNA play pivotal roles in reproductive development, and their biogenesis and action mechanisms are well characterised in angiosperm plants; corresponding studies in conifers are very limited
Twenty-one high-confidence homologues involved in Small RNA (sRNA) biogenesis and action in P. tabuliformis were identified (Table 1)
Our results showed that the important miRNAs and their targets involved in angiosperm reproductive development, such as miR156/miR529-SPLs [50], miR159MYBs [51], miR172-AP2Ls [52], miR319-TCPs [53] and miR396-GRFs [31], coevolved and have an ancient evolutionary history, similar to the sRNA pathways, such as miR156 and miRNA319, which have evolved in moss plants [60]

Summary

Introduction

Small RNA (sRNA) play pivotal roles in reproductive development, and their biogenesis and action mechanisms are well characterised in angiosperm plants; 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). The sRNA pathways in plants mainly include the microRNA (miRNA) and shortinterfering RNA (siRNA) pathways [2]. The miRNAs are a family of small endogenous noncoding single-stranded RNA molecules that regulate gene expression posttranscriptionally by directing mRNA degradation or translational repression and control many biological functions, including development and tissuespecific processes in both plants and animals [4, 5].

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