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Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents

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Preprint: Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents https://t.co/hsbD2OUywU https://t.co/lAbpmM67Yq
Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents https://t.co/r6SrLyIZHN The endosperm is a crucial organ for seeds that plays vital roles in supporting embryo development and determining se…
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Supplemental Information

Reads coverage of the SD609 and HS68 endosperms at the four developmental stages

Supplementary figure 1 Reads coverage of the SD609 and HS68 endosperms at the four developmental stages. From outside to inside of Circos image representing reads of 5, 10, 15 and 20 DAP mapped to maize reference genome sequences. Of which, red colour and green colour represents normalized reads number of SD609 and HS68, respectively.

DOI: 10.7287/peerj.preprints.27577v1/supp-1

Functional enrichment analysis of the shared genes among the four stages of endosperm development in SD609 and HS68

Supplementary figure 2 Functional enrichment analysis of the shared genes among the four stages of endosperm development in SD609 and HS68. (A) The enriched GO terms “biological process”, (B) “cellular component”, and (C) “molecular function” categories are shown.

DOI: 10.7287/peerj.preprints.27577v1/supp-2

Number of DEGs identified in SD609 and HS68

Supplementary figure 3 Number of DEGs identified in SD609 and HS68. A total of 1,193 DEGs were differentially expressed between SD609 and HS68, 7,813 DEGs were consistently expressed at the different development stages of SD609 and HS68, and 4,914 and 2,002 DEGs were specifically detected in SD609 and HS68, respectively.

DOI: 10.7287/peerj.preprints.27577v1/supp-3

Functional enrichment analysis of DEGs at different developmental stages

Supplementary figure 4 Functional enrichment analysis of DEGs at different developmental stages. (A) Functional annotation of 1,193 DEGs between SD609 and HS68. (B) Shared biological processes regulated by the material-specific DEGs of SD609 and HS68. (C) Specific biological processes of HS68 that are regulated by the material-specific DEGs of SD609 and HS68. (D) Specific biological processes of SD609 that are regulated by the material-specific DEGs of SD609 and HS68. Only biological processes with P values<0.0001 and FDR<0.01 are shown.

DOI: 10.7287/peerj.preprints.27577v1/supp-4

Functional enrichment analysis of the DEG sets of the coexpression clusters

Supplementary figure 5 Functional enrichment analysis of the DEG sets of the coexpression clusters. Only biological processes with a P value<0.0001 and FDR<0.01 are shown. (B) Functional analysis of coexpression clusters of SD609. (C) Functional analysis of coexpression clusters of HS68. (A) Functional analysis of shared DEGs in coexpression clusters between SD609 and HS68.

DOI: 10.7287/peerj.preprints.27577v1/supp-5

Expression patterns of shared DEGs between SD609 and HS68

Supplementary figure 6 Expression patterns of shared DEGs between SD609 and HS68. (A) Sixteen clusters were characterized by the fluctuating expression of gene sets at 5, 10, 15 and 20 DAP in both SD609 and HS68. The up- and downregulated gene sets are staggered or depicted consecutively during the developmental stages of the maize endosperm, and the same DEG sets with the same or different expression patterns in two different maize materials are shown. The scaled expression levels of the DEGs are provided on the y-axis, the developmental stages are shown on the x-axis, the coloured lines represent the individual gene expression clusters, and the trend in the expression of each gene set is depicted as a black line. “n” represents the number of DEGs.

DOI: 10.7287/peerj.preprints.27577v1/supp-6

Relationship between module eigengenes

Supplementary figure 7 Relationship between module eigengenes. The diagonals show the distribution. The lower left section shows a bivariate scatterplot with a fitting line, and the upper right section shows the correlation coefficient and the significance level.

DOI: 10.7287/peerj.preprints.27577v1/supp-7

List of primers used for the qRT-PCR gene detection analysis

Supplementary table 1 List of primers used for the qRT-PCR gene detection analysis.

DOI: 10.7287/peerj.preprints.27577v1/supp-8

Statistical analysis of the sequenced and mapped reads of SD609 and HS68

Supplementary table 2 Statistical analysis of the sequenced and mapped reads of SD609 and HS68.

DOI: 10.7287/peerj.preprints.27577v1/supp-9

Information on the expressed genes of SD609 and HS68

Supplementary table 3 Information on the expressed genes of SD609 and HS68.

DOI: 10.7287/peerj.preprints.27577v1/supp-10

Functional enrichment analysis of stage-specific gene expression

Supplementary table 4 Functional enrichment analysis of stage-specific gene expression.

DOI: 10.7287/peerj.preprints.27577v1/supp-11

Information of DEGs from SD609 and HS68

Supplementary table 5 Information of DEGs from SD609 and HS68.

DOI: 10.7287/peerj.preprints.27577v1/supp-12

GO enrichment analysis of the DEGs of SD609 and HS68

Supplementary table 6 GO enrichment analysis of the DEGs of SD609 and HS68.

DOI: 10.7287/peerj.preprints.27577v1/supp-13

qRT-PCR analysis of candidate genes

Supplementary table 7 qRT-PCR analysis of candidate genes.

DOI: 10.7287/peerj.preprints.27577v1/supp-14

Functional annotation of the WGCNA modules

Supplementary table 8 Functional annotation of the WGCNA modules.

DOI: 10.7287/peerj.preprints.27577v1/supp-15

Functional annotation of the hub genes

Supplementary table 9 Functional annotation of the hub genes.

DOI: 10.7287/peerj.preprints.27577v1/supp-16

Starch core gene networks

Supplementary table 10 Starch core gene networks.

DOI: 10.7287/peerj.preprints.27577v1/supp-17

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Zhou Jian Qu conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper.

Tu Shu Xu approved the final draft.

Kang Xiao Tian approved the final draft.

Ting Li approved the final draft.

Cheng Li Wang approved the final draft.

Yue Yu Zhong approved the final draft.

Quan Ji Xue conceived and designed the experiments.

Wei Dong Guo conceived and designed the experiments.

Data Deposition

The following information was supplied regarding data availability:

National Center for Biotechnology Information Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP065059 and SRP149609.

Funding

This work was supported by the Shaanxi Province Science and Technology Innovation Coordination Project (2015KTZDNY01-01-01) and the Natural Key Research and Development Program of China (2017YFD0300304). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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