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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: 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.

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Size distributions of the contigs and unigenes in the American ginseng seed transcriptome.
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pone.0118558.g002: Size distributions of the contigs and unigenes in the American ginseng seed transcriptome.

Mentions: To obtain an overview of the seed transcriptome during the dormancy release process, a cDNA library was generated from RNA isolated from four seed treatments including anatomical development and physiological after-ripening stages, and paired-end sequenced using the Illumina platform. After cleaning and quality checks, approximately 25.86 million clean reads were assembled into 148,244 contigs (Table 1). The mean contig size was 275 bp. Using paired-end joining and gap-filling, these contig were further assembled into 78,207 unique sequences with a mean size of 531 bp. The size distributions of the contigs and unigenes are shown in Fig. 2. The raw transcriptome reads were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (accession number: SRR1586196)


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)

Size distributions of the contigs and unigenes in the American ginseng seed transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0118558.g002: Size distributions of the contigs and unigenes in the American ginseng seed transcriptome.
Mentions: To obtain an overview of the seed transcriptome during the dormancy release process, a cDNA library was generated from RNA isolated from four seed treatments including anatomical development and physiological after-ripening stages, and paired-end sequenced using the Illumina platform. After cleaning and quality checks, approximately 25.86 million clean reads were assembled into 148,244 contigs (Table 1). The mean contig size was 275 bp. Using paired-end joining and gap-filling, these contig were further assembled into 78,207 unique sequences with a mean size of 531 bp. The size distributions of the contigs and unigenes are shown in Fig. 2. The raw transcriptome reads were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (accession number: SRR1586196)

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