Open Access Highly Accessed Research article

Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq

Guoqin Liu12, Wanshun Li3, Penghua Zheng1, Tong Xu3, Lijuan Chen3, Dongfeng Liu1, Sayed Hussain1 and Yuanwen Teng1*

Author Affiliations

1 Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China

2 College of Agriculture, Guizhou University, Guiyang, 550025,, Guizhou Province, China

3 BGI-tech, Shenzhen, 518083,, Guangdong Province, China

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BMC Genomics 2012, 13:700  doi:10.1186/1471-2164-13-700

Published: 12 December 2012

Additional files

Additional file 1:

Overview of 'Suli' pear (Pyrus pyrifoliawhite pear group) transcriptome sequencing and assembly. (A) Size distribution of Illumina sequencing contigs. (B) Size distribution of unigenes after paired-end and gap filling.

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Additional file 2:

Primers used in RT-PCR to evaluate the quality of unigene sequencing data.

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Additional file 3:

Top BLAST hits from the four public database (nr, SwissProt, KEGG, and GO).

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Additional file 4:

The 29,500 unigenes assigned to 128 KEGG pathways.

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Additional file 5:

Sequencing saturation analysis of the four libraries. All libraries approached saturation as the number of reads approached 5 million, as indicated by the decline in the number of new genes detected.

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Additional file 6:

Distribution of reads on reference genes. All libraries showed good levels of randomness, with the number of reads evenly distributed throughout the transcriptomes.

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Additional file 7:

Differentially-expressed genes between the Nov. 15 and Dec. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Dec. 15-RPKM/Nov. 15-RPKM). Up-Down-Regulation (Dec. 15/Nov. 15): Dec. 15 is a up/down regulation relative to Nov. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

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Additional file 8:

Differentially-expressed genes between the Nov. 15 and Jan. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Jan. 15-RPKM/Nov. 15-RPKM). Up-Down-Regulation (Jan. 15/Nov. 15): Jan. 15 is a up/down regulation relative to Nov. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

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Additional file 9:

Differentially-expressed genes between the Nov. 15 and Feb. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Feb. 15-RPKM/Nov. 15-RPKM). Up-Down-Regulation (Feb. 15/Nov. 15): Feb. 15 is a up/down regulation relative to Nov. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

Format: XLS Size: 403KB Download file

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Additional file 10:

Differentially-expressed genes between the Dec. 15 and Jan. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Jan. 15-RPKM/Dec. 15-RPKM). Up-Down-Regulation (Jan. 15/Dec. 15): Jan. 15 is a up/down regulation relative to Dec. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

Format: XLS Size: 195KB Download file

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Additional file 11:

Differentially-expressed genes between the Dec. 15 and Feb. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Feb. 15-RPKM/Dec. 15-RPKM). Up-Down-Regulation (Feb. 15/Dec. 15): Feb. 15 is a up/down regulation relative to Dec. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

Format: XLS Size: 645KB Download file

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Additional file 12:

Differentially-expressed genes between the Jan. 15 and Feb. 15 libraries. Genelength: length of all exon in gene. Expression: unique reads of aligned reads. RPKM: Reads Per Kb per Million reads. log2 Ratio: log2 (Feb. 15-RPKM/Jan. 15-RPKM). Up-Down-Regulation (Feb. 15/Jan. 15): Feb. 15 is a up/down regulation relative to Jan. 15. P-value: pvalue for hypothesis testing. FDR: false discovery rate. We used FDR ≤ 0.001 and the absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of gene expression difference.

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Additional file 13:

The top 20 most up-regulated and down-regulated DEGs between samples (Nov. 15-VS-Dec. 15, Dec. 15-VS-Jan. 15 and Jan. 15-VS-Feb. 15). RPKM: Reads Per Kb per Million reads. DEGs: Differentially-expressed genes with the expression fold (log2Ratio ≥ 2) and false discovery rate (FDR ≤ 10-5) as the threshold.

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Additional file 14:

KEGG pathways significantly enriched during dormancy. KEGG pathways significantly enriched were defined as pathways with Q-value ≤ 0.05.

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Additional file 15:

190 genes differentially expressed during dormancy. In total, 190 genes were found that were significantly differentially-expressed genes between Nov. 15 and Dec. 15, between Dec. 15 and Jan. 15, and between Jan. 15 and Feb. 15. 190 genes with annotations and their expression fold between Nov. 15 and Dec. 15, between Dec. 15 and Jan. 15, and between Jan. 15 and Feb. 15.

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Additional file 16:

Primers used in Q-PCR to validate differential expression during pear dormancy.

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