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Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberry (Fragaria × ananassa)

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Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberry (Fragaria × ananassa) https://t.co/fvng4BcCt1
Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberry (Fragaria × ananassa) https://t.co/a7ngWadQX2 Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and …
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Supplemental Information

URLs, annotation methods and parameters of seven databases

The comprehensive information of gene function comes from seven databases.

DOI: 10.7287/peerj.preprints.26870v1/supp-1

The information of software version and parameter

Each data indicate the information of software that produces all the transcriptome data.

DOI: 10.7287/peerj.preprints.26870v1/supp-2

The distribution of FPKM values of each library

FPKM: fragments per kilobaseof exon per million fragments mapped. FPKM is the most commonly used method of estimating gene expression level, which eliminates the expression level of technical deviation.

DOI: 10.7287/peerj.preprints.26870v1/supp-3

Primers used in this study

Each data indicates the detail information of candidate genes in quantitative real-time polymerase chain reaction.

DOI: 10.7287/peerj.preprints.26870v1/supp-4

The annotation results of KOG classification

Each data indicates the annotation result in seven databases.

DOI: 10.7287/peerj.preprints.26870v1/supp-5

The GO classification of unigenes

Each data indicates the classification of unigenes in GO database.

DOI: 10.7287/peerj.preprints.26870v1/supp-6

The KOG classification of unigenes

Each data indicates the classification of unigenes in KOG database.

DOI: 10.7287/peerj.preprints.26870v1/supp-7

The KEGG classification of unigenes

Each data indicates the classification of unigenes in KEGG database.

DOI: 10.7287/peerj.preprints.26870v1/supp-8

Differential analysis results of genes in different combinations

Each data is used to determine the differentially expressed genes (DEGs). The DEGs with padj < 0.05 and log2 (fold change) ≥ 1 are up-regulated, and those with padj < 0.05 and log2 (fold change) ≤ -1 are down-regulated. The other genes that do not meet the conditions of padj < 0.05 and log2 (fold change)| ≥ 1 are not DEGs.

DOI: 10.7287/peerj.preprints.26870v1/supp-9

Detailed information of genes in the flavonoid biosynthesis pathway

Each data indicates the average read_count of genes in each library.

DOI: 10.7287/peerj.preprints.26870v1/supp-10

Detailed information of genes in results

Each data indicates the corrected read_count value, differential analysis results and annotation information of genes in each library.

DOI: 10.7287/peerj.preprints.26870v1/supp-11

FPKM interval of all samples

FPKM: fragments per kilobaseof exon per million fragments mapped. The percentage of each sample's corresponding FPKM interval can be used to measure the difference in expression between samples.

DOI: 10.7287/peerj.preprints.26870v1/supp-12

Length distribution of transcripts and unigenes

The x-axis represents the length interval of transcript/unigene, and the y-axis represents the number of times for each length of the transcript/unigene.

DOI: 10.7287/peerj.preprints.26870v1/supp-13

Characteristics of homology search of Illumina sequences against the Nr database

(A) Percentage of the total homologous sequences of 5 top species against the Nr database; (B) E-value distribution of the top BLASTx hits against the Nr database; (C) Similarity distribution of the top BLASTx hits for each sequence.

DOI: 10.7287/peerj.preprints.26870v1/supp-14

Expression pattern of genes in the flavonoid biosynthetic pathway

(A) Cluster analysis of genes in flavonoid biosynthetic pathway. Expression level was showed by different colors, the redder the higher expression and the bluer the lower. The values of red to blue is log10 (read_count). (B) The relative expression of up- and down-regulated genes in flavonoid biosynthetic pathway. (C) The expression pattern of DEGs in flavonoid biosynthetic pathway.

DOI: 10.7287/peerj.preprints.26870v1/supp-15

Expression pattern of MYB and bHLH transcription factors

(A/C) The relative expression of up- and down-regulated MYB and bHLH transcription factors. Black Fonts indicate the up-regulated gene ID. (B/D) The expression pattern of DEGs of MYB and bHLH transcription factors.

DOI: 10.7287/peerj.preprints.26870v1/supp-16

The expression level of candidate genes in transcriptome data

Each data indicates the expression pattern of candidate genes with strawberry ripening in transcriptome data.

DOI: 10.7287/peerj.preprints.26870v1/supp-17

Expression pattern of genes in starch and sucrose biosynthesis and citrate cycle

(A/B) The relative expression of up- and down-regulated genes in starch and sucrose biosynthesis. (C-E) The expression pattern of DEGs in starch and sucrose biosynthesis. (F) The relative expression of up- and down-regulated genes in citrate cycle. (G) The expression pattern of DEGs in citrate cycle.

DOI: 10.7287/peerj.preprints.26870v1/supp-18

The assembled unigene transcriptome data of unigene sequences

This file showed the sequences of unigenes in this text.

DOI: 10.7287/peerj.preprints.26870v1/supp-19

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Panpan Hu performed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft.

Gang Li contributed reagents/materials/analysis tools, approved the final draft.

Xia Zhao contributed reagents/materials/analysis tools, approved the final draft.

Fengli Zhao approved the final draft, manage and provide the materials.

Liangjie Li approved the final draft, manage and provide the materials.

Houcheng Zhou conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

https://www.ncbi.nlm.nih.gov/sra/?term=SRP111905

Funding

The research was supported by the Central Public-interest Scientific Institution Basal Research Fund (1610192016608, 1612382017204), the Natural Science Foundation of Henan Province (162300410329), and the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2017-ZFRI). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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