Limits...
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: 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.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

Semi-quantitative PCR analysis of 23 selected genes from the American ginseng seeds libraries.M: maker; 0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4366157&req=5

pone.0118558.g006: Semi-quantitative PCR analysis of 23 selected genes from the American ginseng seeds libraries.M: maker; 0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.

Mentions: Many reports have shown that stratification can lead to increased expression of the gibberellic acid (GA) biosynthesis genes GA20ox and GA3ox, but deceased expression of the GA catabolic gene GA2ox in Arabidopsis seeds [31, 32]. Additional studies have identified specific genes correlated with dormancy maintenance (NCED, ZEP (zeaxanthin epoxidase) and ABI (ABA insensitive)) and dormancy release via ABA catabolism (CYP707A) [33–35]. In this work, we evaluated the DGE library using 30 unigenes including those that were associated with GA and ABA, as well as DELLA (a negative regulator of GA signal), ACC (1-aminocyclopropane-1-carboxylate synthase), GIGATEA, PICKLE (CHD3-type chromatin-remodeling factor PICKLE), KAO (Ent-kaurenoic acid oxidase), and CTR(serine/threonine-protein kinase CTR1) and others [36–38]. For the semi-quantitative PCR analysis, 41 primers were designed for the 30 unigenes (the primers are listed in S1 Table). Twenty-three of the primers successful amplified 23 of the 30 selected unigenes (Fig. 6). The PCR data for 19 of the 23 amplified (the exceptions were GA2ox2, GA2ox3, GA3ox2, and GA20ox1) were basically consistent with the RNA-Seq data for the 90DAS, 135DAS and 180DAS samples (Table 4). We also analyzed the expression levels of these 23 unigenes on Day 0 and 45 of the warm stratification and in three control tissues (root, stem, and leaf). The results showed that almost all unigenes had no or weak expression in the early stage (0 days) of seed stratification.


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)

Semi-quantitative PCR analysis of 23 selected genes from the American ginseng seeds libraries.M: maker; 0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0118558.g006: Semi-quantitative PCR analysis of 23 selected genes from the American ginseng seeds libraries.M: maker; 0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
Mentions: Many reports have shown that stratification can lead to increased expression of the gibberellic acid (GA) biosynthesis genes GA20ox and GA3ox, but deceased expression of the GA catabolic gene GA2ox in Arabidopsis seeds [31, 32]. Additional studies have identified specific genes correlated with dormancy maintenance (NCED, ZEP (zeaxanthin epoxidase) and ABI (ABA insensitive)) and dormancy release via ABA catabolism (CYP707A) [33–35]. In this work, we evaluated the DGE library using 30 unigenes including those that were associated with GA and ABA, as well as DELLA (a negative regulator of GA signal), ACC (1-aminocyclopropane-1-carboxylate synthase), GIGATEA, PICKLE (CHD3-type chromatin-remodeling factor PICKLE), KAO (Ent-kaurenoic acid oxidase), and CTR(serine/threonine-protein kinase CTR1) and others [36–38]. For the semi-quantitative PCR analysis, 41 primers were designed for the 30 unigenes (the primers are listed in S1 Table). Twenty-three of the primers successful amplified 23 of the 30 selected unigenes (Fig. 6). The PCR data for 19 of the 23 amplified (the exceptions were GA2ox2, GA2ox3, GA3ox2, and GA20ox1) were basically consistent with the RNA-Seq data for the 90DAS, 135DAS and 180DAS samples (Table 4). We also analyzed the expression levels of these 23 unigenes on Day 0 and 45 of the warm stratification and in three control tissues (root, stem, and leaf). The results showed that almost all unigenes had no or weak expression in the early stage (0 days) of seed stratification.

Bottom Line: 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.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