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

BMC Genomics

Research Article

Bing Zhang¹  Songnian Hu¹  Xianen Li²  Peng Sun²  Lili Zhou²  Wenjuan Xu²  Jianjun Qi²  Na Zheng³  Mingjian Qin⁴  Tingzhou Zhao⁵  Qin Ma⁵ 

[1] Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, 100029, Beijing, Chaoyang District, China;Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No.151 Malianwa North Road, 100193, Beijing, Haidian District, China;Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No.151 Malianwa North Road, 100193, Beijing, Haidian District, China;School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, 210009, Nanjing, China;School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, 210009, Nanjing, China;Yunnan BaiYao Group Co. Ltd, 3686 BaiYao Street, 650500, Kunming, ChengGong District, China;

关键词: Embryo;    Stratification;    Seed dormancy;    High-throughput sequencing;    Paris polyphylla;   

DOI  :  10.1186/1471-2164-14-358

 received in 2012-10-15, accepted in 2013-05-27,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundParis 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.ResultsIn 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.ConclusionsGene 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.

【 授权许可】

Unknown   
© Qi et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.