Global transcriptomics identification and analysis of transcriptional factors in different tissues of the paper mulberry.

Peng Xianjun,Shen Shihua,Wang Yucheng,Zhao Meiling,He Ruiping

doi:10.1186/s12870-014-0194-6

Abstract

BackgroundThe paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is also commonly utilized in traditional medicine in China and other Asian countries. To identify the transcription factors (TFs) and comprehensively understand their regulatory roles in the growth of the paper mulberry, a global transcriptomics TF prediction and the differential expression analysis among root, shoot and leaf were performed by using RNA-seq.ResultsResults indicate that there is 1,337 TFs encoded by the paper mulberry and they belong to the 55 well-characterized TF families. Based on the phylogenetic analysis, the TFs exist extensively in all organisms are more conservative than those exclusively exist in plant and the paper mulberry has the closest relationship with the mulberry. According to the results of differential expression analysis, there are 627 TFs which exhibit the differential expression profiles in root, shoot and leaf. ARR-Bs, ARFs, NACs and bHLHs together with other root-specific and highly expressed TFs might account for the developed lateral root and unconspicuous taproot in the paper mulberry. Meanwhile, five TCPs highly expressed in shoot of the paper mulberry might negatively regulate the expression of 12 LBDs in shoot. Besides, LBDs, which could directly or indirectly cooperate with ARFs, bHLHs and NACs, seem to be the center knot involving in the regulation of the shoot development in the paper mulberry.ConclusionsOur study provides the comprehensive transcriptomics identification of TFs in the paper mulberry without genome reference. A large number of lateral organ growth regulation related TFs exhibiting the tissue differential expression may entitle the paper mulberry the developed lateral roots, more branches and rapid growth. It will increase our knowledge of the structure and composition of TFs in tree plant and it will substantially contribute to the improving of this tree.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0194-6) contains supplementary material, which is available to authorized users.

Highlights

The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is commonly utilized in traditional medicine in China and other Asian countries
Identification and classification of transcription factors (TFs) in the paper mulberry To ascertain the TF families in the paper mulberry, sequences obtained from 3 libraries as mentioned in the materials and methods were assembled
After retrieving annotation results for every unigene, 1,337 TFs were identified and classified into 55 families (Table 1) based on their DNA-binding domains and other conserved motifs [18,19]. Of these TFs, 578 TFs belonged to 48 families with complete ORF (Table 2)

Summary

Introduction

The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is commonly utilized in traditional medicine in China and other Asian countries. To identify the transcription factors (TFs) and comprehensively understand their regulatory roles in the growth of the paper mulberry, a global transcriptomics TF prediction and the differential expression analysis among root, shoot and leaf were performed by using RNA-seq. The paper mulberry has shallow roots with advanced lateral roots and without an obvious taproot. It is one of the multifunctional tree species in agroforestry systems [1], as well as being one of the traditional forages [2] and Chinese medicines in many countries of Asia [3]. Many TF family proteins, such as bHLH [7], ERF [8], Dof [9], MYB [10], NAC [11] and WRKY [12], play regulatory roles in plants growth and development

Methods

Results

Discussion

Conclusion