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Anatomical and transcriptional dynamics of early floral development of mulberry (Morus alba)

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Abstract

Sex determination of flowers is a critical component of reproductive biology in plants. The plant hormone ethylene promotes female flower formation in mulberry. Illumina RNA-Seq technology was used for de novo transcriptome assembly to compare the gene expression profiling from six early floral bud stages of mulberry flowers. A set of 87,719 unigenes were generated from 6 different stages in flower bud development. Differential gene expression analysis revealed that the transcriptomes from flower buds of the two early stages (FB2 and FB3) were very different from the remaining. There were 317 genes upregulated in FB2 to FB1. For FB3 and FB4, there were 122 genes upregulated and 328 genes downregulated. We also analyzed several genes and gene families that were previously shown to be involved in floral bud development. Quite a few AP2/ERF genes showed higher expression in both FB2 and FB3. Most of MADS genes showed a gradually increasing expression profile. A gene that belonged to the family of the ethylene biosynthesis genes, 1-aminocyclopropane-1-carboxylate synthase (ACS), showed a rapid rise in FB2, followed by a slow decline. Two genes (MaDREB-A1-1b and MaDREB-A1-1a) were upregulated by ethephon treatment, suggesting a response to ethylene signal during early development of floral bud. The co-expression patterns of genes were also analyzed, along with associated genes previously identified to be important in floral initiation and development. Our dataset provides a rich resource for the analysis of mulberry early floral development.

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Acknowledgements

This project was funded by the research grants from the National Hi-Tech Research and Development Program of China (No. 2013AA100605-3), Natural Science Foundation of China (No. 31572323), China Postdoctoral Science Foundation funded projects (No. 2013 M540694 and No. 2014 T70845), and the “111” Project (B12006).

Author’s contribution statement

NH and JS conceived and designed the research. JS prepared the samples and analyzed the data. JS and NH conducted the experiments and wrote the paper. JL and ZX contributed new reagents and analytical tools. NH and JL revised the manuscript. All authors read and approved the manuscript.

Author information

Correspondence to Ningjia He.

Additional information

Data archiving statement

The datasets reported in this paper have been deposited as raw reads in the Genbank SRA database (accession number SRR2868676). The BioProject ID related to this paper is PRJNA272494.

Communicated by M. Wirthensohn

Electronic supplementary material

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Fig. S1

Expression correlations between flower buds. Abscissa: the value of sample1 was calculated using log10 (FPKM + 1). Ordinate: the value of sample2 was calculated using log10 (FPKM + 1). R 2, Pearson correlation coefficient. FB, flower bud (GIF 32 kb)

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Fig. S2

Venn diagram depicting the overlap of DEG genes between two flower buds. The DEGs include both up and down-regulated genes in flower buds. A, the DEGs of between two adjacent time point floral buds. B, the DEGs of between the other time points against FB1. (GIF 16 kb)

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Fig. S3

KEGG enriched in DEGs of between two adjacent time point floral buds. Benjamini-Hochberg-adjusted P values (q-value <0.05) are shown. (GIF 12 kb)

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Fig. S4

FB1-FB2 DEGs KEGG enrichment in plant hormone signal transduction. Red: up-regulated genes, green: down-regulated genes (GIF 26 kb)

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Fig. S5

FB3-FB4 DEGs KEGG enrichment in plant hormone signal transduction. Red: up-regulated genes, green: down-regulated genes (GIF 26 kb)

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Fig. S6

Expression patterns of hormone-related genes. For each hormone, its related genes are divided into two functional categories: (1) synthesis-degradation, (2) signal transduction. The FPKM values were used. All the values were converted by log10 (FPKM + 1) and normalized by scale function of R program. (GIF 333 kb)

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Fig. S7

The expression of floral initiation genes. A, The current known components and relationships of floral initiation in Arabidopsis. B, Expression patterns of putative mulberry orthologs of A. thaliana floral initiation. The FPKM of floral initiation genes were used. These genes were identified by BLAST method. (GIF 77 kb)

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Fig. S8

Co-expression patterns with specific genes. Co-expression analysis of the transcript used the WGCNA package of R. Calculate the correlation between each two genes. According to the correlation, the genes were divided into different expression patterns. The correlation between expression pattern and the expression of gene marked in each small box. P1–27, highly similar expression patterns. AP2/ERF family genes were mainly expressed in the FB2 and FB3. The expression of MADS-boxes genes were gradual increased during floral bud development. (GIF 215 kb)

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Fig. S9

KEGG analysis of P19 and P24 module genes. Rich_factor, input number/background number; q value, Benjamini-Hochberg-adjusted P values. (GIF 43 kb)

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Fig. S10

Co-expression network comprehensive analysis of P24. The yellow ellipse represent the gene have more than 40 links. The red ellipse represent the genes have between 20 and 40 links. The green ellipse represent the genes have between 10 and 20 links. (GIF 68 kb)

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Fig. S11

Verification of differentially expressed genes by qRT-PCR. Relative levels of gene expression by qRT-PCR were normalized against the mulberry ribosomal protein gene Morus024083. Data are represented as mean ± standard error of three replicates. (GIF 23 kb)

High resolution image (TIFF 180 kb)

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Shang, J., Liang, J., Xiang, Z. et al. Anatomical and transcriptional dynamics of early floral development of mulberry (Morus alba). Tree Genetics & Genomes 13, 40 (2017). https://doi.org/10.1007/s11295-017-1122-3

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Keywords

  • RNA-seq
  • Early floral bud
  • Development
  • Mulberry
  • Ethylene