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. 2014 Aug 20:14:194.
doi: 10.1186/s12870-014-0194-6.

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

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

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

Peng Xianjun et al. BMC Plant Biol. .

Abstract

Background: The 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.

Results: Results 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.

Conclusions: Our 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.

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Figures

Figure 1
Figure 1
Evolutionary relationships revealed by phylogenetic analysis of CAMTA, Whirly and VOZ family. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1500 replicates) was shown next to the branches. The tree was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method and were in the units of the number of amino acid differences per site. The analysis involved 74 CAMTAs (A), 29 Whirlys (B) and 27 VOZs (C) amino acid sequences and their correspondent accession numbers were list in Additional file 4: Table S6. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA5.
Figure 2
Figure 2
Venn diagram of TFs expressed and differently expressed in root, shoot and leaf. A Venn diagram of TFs expressed in root, shoot and leaf. B Venn diagram of differentially expressed TFs in root, shoot and leaf. TFs differentially expressed in root, shoot and leaf were identified. To be considered differentially expressed, the transcript must have RPKM ≥ 2 in at least one tissue, 2-fold or greater change between tissues, and P ≤ 0.05.
Figure 3
Figure 3
The differentially expressed TFs distributed in each family. According to the conserved domain, a total of 627 differentially expressed TFs could be classified into 50 families and most of them concentrated in bHLH, MYB, WRKY, C2H2, NAC, C3H, B3 and Dof family.
Figure 4
Figure 4
The cluster analysis of the differentially expressed TFs in root, shoot and leaf of the paper mulberry. A The TFs highly expressed in shoot than that in leaf and root. B The TFs highly expressed in leaf than that in shoot and root. C The TFs highly expressed in root than that in leaf and shoot. The pink line represented the expression trend of the cluster. The gray line represented the expression profile of every TF.
Figure 5
Figure 5
The expression profile of ten selected TFs validated by qPCR. The left axis represents the results of transcriptomics analysis while the right axis represents relative expression detected by qPCR, and the error bars represented the standard deviation (S.D.) values for three independent experiments, performed in triplicate.
Figure 6
Figure 6
The total number of TFs in the selected species. The TF numbers of Arabidopsis thaliana, Cannabis sativa, Fragaria vesca, Oryza sativa subsp. Japonica and Vitis vinifera were obtained from Plant Transcription Factor Database (http://planttfdb.cbi.pku.edu.cn/index.php).
Figure 7
Figure 7
Heat map of expression profiles of TFs involved in the differential expression among root, shoot and leaf. Red indicates high expression, black indicates intermediate expression, and green indicates low expression. To be considered differentially expressed, the transcript must have RPKM ≥ 2 in at least one tissue, 2-fold or greater change between tissues, and P ≤ 0.05. TFs have been grouped by family.
Figure 8
Figure 8
The proposed TFs involved in tissues development and growth of the paper mulberry. The arrow lines stand for the effect of activation. The “T” lines stand for the effects of inhibition. The dotted lines stand for the unknown effects.
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