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

PloS One
Jianjun QiXianen Li

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 ...Continue Reading

References

Oct 23, 1997·Genome Research·S Audic, J M Claverie
Aug 11, 1998·Immunology Letters·Y H ChenM P Dierich
Aug 2, 2000·Proceedings of the National Academy of Sciences of the United States of America·E HuqP H Quail
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Nov 2, 2002·The Plant Journal : for Cell and Molecular Biology·Luis Lopez-MolinaNam-Hai Chua
Mar 2, 2006·The Plant Journal : for Cell and Molecular Biology·Anthony A MillarFrank Gubler
May 20, 2006·The Plant Journal : for Cell and Molecular Biology·Cassandra S C CadmanWilliam E Finch-Savage
Jul 18, 2006·Nucleic Acids Research·Jia YeJun Wang
Feb 9, 2008·Annual Review of Plant Biology·Ruth FinkelsteinCamille Steber
Mar 22, 2008·Applied Microbiology and Biotechnology·Takumi SuizuMakoto Kawamukai
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Sep 16, 2010·BMC Plant Biology·Peter E HedleyRex Brennan
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Apr 27, 2012·The Biochemical Journal·Peter Hedden, Stephen G Thomas
Jan 25, 2014·BMC Genomics·Wenqin WangJoachim Messing

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Citations

Feb 6, 2017·Protoplasma·Jeniffer SilvaDabing Zhang
Feb 26, 2019·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Musa KavasHüseyin İrfan Balık
Apr 24, 2021·Frontiers in Genetics·Rakesh KumarAnirudh Kumar

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Datasets Mentioned

BETA
SRR1586196

Methods Mentioned

BETA
454-sequencing
454 sequencing
RNA-Seq
PCR

Software Mentioned

Blast2GO
BLASTX
ESTScan
WEGO
SOAPaligner
Trinity
BLASTALL

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