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Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq.

Qi J, Sun P, Liao D, Sun T, Zhu J, Li X - PLoS ONE (2015)

Bottom Line: Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release.There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared.This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.

ABSTRACT
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.

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Venn diagram showing number of DEGs revealed by paired comparison (FDR≤0.001, /log2FC/≥1).The numbers of up- and down-regulated genes in comparisons of 135DAS/90DAS, 180DAS/135DAS/, and 180DAS/90DAS libraries. DEGs: Differentially expressed genes.
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pone.0118558.g005: Venn diagram showing number of DEGs revealed by paired comparison (FDR≤0.001, /log2FC/≥1).The numbers of up- and down-regulated genes in comparisons of 135DAS/90DAS, 180DAS/135DAS/, and 180DAS/90DAS libraries. DEGs: Differentially expressed genes.

Mentions: Differences in gene expression among the three seed dormancy stages during the cold stratification were examined, and differentially expressed genes (DEGs) were identified by the pairwise comparisons: 90DAS-VS-135DAS, 90DAS-VS-180DAS, and 135DAS-VS-180DAS. Fig. 5 (a) and (b) showed the distribution of the total number of DEGs up- or down-regulated between two compared stages and their relationship among the different comparisons. 3635 and 3037 DEGs were found to be up- and down-regulated separately in the 135DAS to 90DAS comparison. A similar number of DEGs were differentially expressed between 180DAS and 90DAS. The comparison of 180DAS and 135DAS identified 2096 enhanced DEGs and 1774 decreased DEGs, which were less than the former two comparisons, indicating less genes showed differential expression through 135DAS to 180DAS. Only the expression abundance of 368 and 182 DEGs were significantly increased or decreased by at least 2 folds throughout the cold stratification, indicating that most transcripts were transiently significantly regulated by the switches of stratification process. For example, of 3635 enhanced Unigenes in 135DAS to 90DAS comparison, 1224 Unigenes were increased only in 135DAS, and 2043 Unigenes were overlapped with those in 180DAS to 90DAS comparison, indicating that they still remained higher expression levels in 180DAS after the increase since 135DAS, but no quantitative difference from 135DAS. These differences in gene expression are consistent with the seed dormancy release process. Some reports have shown that gene activity was lowest in the early stages of dormancy and peaked around the time of dormancy break [24, 30]. In the 90DAS, 135DAS and 180DAS libraries, 21.38%, 17.67%, and 25.58% genes, respectively, found no matches in the nr or GO databases. These genes may be candidates for future investigations.


Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq.

Qi J, Sun P, Liao D, Sun T, Zhu J, Li X - PLoS ONE (2015)

Venn diagram showing number of DEGs revealed by paired comparison (FDR≤0.001, /log2FC/≥1).The numbers of up- and down-regulated genes in comparisons of 135DAS/90DAS, 180DAS/135DAS/, and 180DAS/90DAS libraries. DEGs: Differentially expressed genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366157&req=5

pone.0118558.g005: Venn diagram showing number of DEGs revealed by paired comparison (FDR≤0.001, /log2FC/≥1).The numbers of up- and down-regulated genes in comparisons of 135DAS/90DAS, 180DAS/135DAS/, and 180DAS/90DAS libraries. DEGs: Differentially expressed genes.
Mentions: Differences in gene expression among the three seed dormancy stages during the cold stratification were examined, and differentially expressed genes (DEGs) were identified by the pairwise comparisons: 90DAS-VS-135DAS, 90DAS-VS-180DAS, and 135DAS-VS-180DAS. Fig. 5 (a) and (b) showed the distribution of the total number of DEGs up- or down-regulated between two compared stages and their relationship among the different comparisons. 3635 and 3037 DEGs were found to be up- and down-regulated separately in the 135DAS to 90DAS comparison. A similar number of DEGs were differentially expressed between 180DAS and 90DAS. The comparison of 180DAS and 135DAS identified 2096 enhanced DEGs and 1774 decreased DEGs, which were less than the former two comparisons, indicating less genes showed differential expression through 135DAS to 180DAS. Only the expression abundance of 368 and 182 DEGs were significantly increased or decreased by at least 2 folds throughout the cold stratification, indicating that most transcripts were transiently significantly regulated by the switches of stratification process. For example, of 3635 enhanced Unigenes in 135DAS to 90DAS comparison, 1224 Unigenes were increased only in 135DAS, and 2043 Unigenes were overlapped with those in 180DAS to 90DAS comparison, indicating that they still remained higher expression levels in 180DAS after the increase since 135DAS, but no quantitative difference from 135DAS. These differences in gene expression are consistent with the seed dormancy release process. Some reports have shown that gene activity was lowest in the early stages of dormancy and peaked around the time of dormancy break [24, 30]. In the 90DAS, 135DAS and 180DAS libraries, 21.38%, 17.67%, and 25.58% genes, respectively, found no matches in the nr or GO databases. These genes may be candidates for future investigations.

Bottom Line: Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release.There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared.This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.

ABSTRACT
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.

Show MeSH
Related in: MedlinePlus