Open Access Highly Accessed Research article

Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing

Jianjun Qi1, Na Zheng12, Bing Zhang3, Peng Sun1, Songnian Hu3, Wenjuan Xu1, Qin Ma4, Tingzhou Zhao4, Lili Zhou1, Mingjian Qin2 and Xianen Li1*

Author Affiliations

1 Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No.151 Malianwa North Road, Beijing, Haidian District 100193, China

2 School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China

3 Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, Beijing, Chaoyang District, 100029, China

4 Yunnan BaiYao Group Co. Ltd, 3686 BaiYao Street, Kunming, ChengGong District, 650500, China

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BMC Genomics 2013, 14:358  doi:10.1186/1471-2164-14-358

Published: 29 May 2013



Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little genomic or transcriptome data are available for this plant.


In this study, massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform was used to generate a substantial sequence dataset for the P. polyphylla embryo. 369,496 high quality reads were obtained, ranging from 50 to 1146 bp, with a mean of 219 bp. These reads were assembled into 47,768 unigenes, which included 16,069 contigs and 31,699 singletons. Using BLASTX searches of public databases, 15,757 (32.3%) unique transcripts were identified. Gene Ontology and Cluster of Orthologous Groups of proteins annotations revealed that these transcripts were broadly representative of the P. polyphylla embryo transcriptome. The Kyoto Encyclopedia of Genes and Genomes assigned 5961 of the unique sequences to specific metabolic pathways. Relative expression levels analysis showed that eleven phytohormone-related genes and five other genes have different expression patterns in the embryo and endosperm in the seed stratification process.


Gene annotation and quantitative RT-PCR expression analysis identified 464 transcripts that may be involved in phytohormone catabolism and biosynthesis, hormone signal, seed dormancy, seed maturation, cell wall growth and circadian rhythms. In particular, the relative expression analysis of sixteen genes (CYP707A, NCED, GA20ox2, GA20ox3, ABI2, PP2C, ARP3, ARP7, IAAH, IAAS, BRRK, DRM, ELF1, ELF2, SFR6, and SUS) in embryo and endosperm and at two temperatures indicated that these related genes may be candidates for clarifying the molecular basis of seed dormancy in P. polyphlla var. yunnanensis.

Embryo; Stratification; Seed dormancy; High-throughput sequencing; Paris polyphylla