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

BACKGROUND: 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. RESULTS: In thi...

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Autores principales: Qi, Jianjun, Zheng, Na, Zhang, Bing, Sun, Peng, Hu, Songnian, Xu, Wenjuan, Ma, Qin, Zhao, Tingzhou, Zhou, Lili, Qin, Mingjian, Li, Xianen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679829/
https://www.ncbi.nlm.nih.gov/pubmed/23718911
http://dx.doi.org/10.1186/1471-2164-14-358
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author Qi, Jianjun
Zheng, Na
Zhang, Bing
Sun, Peng
Hu, Songnian
Xu, Wenjuan
Ma, Qin
Zhao, Tingzhou
Zhou, Lili
Qin, Mingjian
Li, Xianen
author_facet Qi, Jianjun
Zheng, Na
Zhang, Bing
Sun, Peng
Hu, Songnian
Xu, Wenjuan
Ma, Qin
Zhao, Tingzhou
Zhou, Lili
Qin, Mingjian
Li, Xianen
author_sort Qi, Jianjun
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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spelling pubmed-36798292013-06-13 Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing Qi, Jianjun Zheng, Na Zhang, Bing Sun, Peng Hu, Songnian Xu, Wenjuan Ma, Qin Zhao, Tingzhou Zhou, Lili Qin, Mingjian Li, Xianen BMC Genomics Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. BioMed Central 2013-05-29 /pmc/articles/PMC3679829/ /pubmed/23718911 http://dx.doi.org/10.1186/1471-2164-14-358 Text en Copyright © 2013 Qi et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Research Article
Qi, Jianjun
Zheng, Na
Zhang, Bing
Sun, Peng
Hu, Songnian
Xu, Wenjuan
Ma, Qin
Zhao, Tingzhou
Zhou, Lili
Qin, Mingjian
Li, Xianen
Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title_full Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title_fullStr Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title_full_unstemmed Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title_short Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing
title_sort mining genes involved in the stratification of paris polyphylla seeds using high-throughput embryo transcriptome sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679829/
https://www.ncbi.nlm.nih.gov/pubmed/23718911
http://dx.doi.org/10.1186/1471-2164-14-358
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