[논문]차세대염기서열 분석을 이용한 고려인삼과 미국삼의 전사체 분석

조익현; 김영창; 이승호; 김장욱; 김선태; 현동윤; 김동휘; 김기홍; 김홍식; 정종욱; 방경환

doi:10.7783/kjmcs.2014.22.5.339

차세대염기서열 분석을 이용한 고려인삼과 미국삼의 전사체 분석
Characterization of Root Transcriptome among Korean Ginseng Cultivars and American Ginseng using Next Generation Sequencing 원문보기

韓國藥用作物學會誌 = Korean journal of medicinal crop science, v.22 no.5, 2014년, pp.339 - 348

Abstract ▼ AI-Helper

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong (Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95 Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST search against the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotated and classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as well as in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembrane transporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgor pressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantly detected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefolius accession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuable resource for understanding the structure and function of the ginseng transcriptomes.

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제안 방법

A detailed GO analysis at the cellular component category, sorted all transcripts from 4 ginseng accessions into 5 groups being the most the most abundant GO term was ‘cell part’ followed by ‘intracellular’, ‘intracellular part’, ‘intracellular organelle’ and ‘membrane-bounded organelle’ (Fig. 3).
In this study, we analyzed transcriptome sequencing of 4-year-old P. ginseng and P. quinquefolius roots. Novel and tissue-specific P.

대상 데이터

The experiment was conducted at the field of National Institute of Horticultural and Herbal Science (NIHHS) of Rural Development Administration (RDA) in Eumsung (127o 45' 13.14" E, 36o 56' 36.63" N), Republic of Korea.
quinquefolius accession was preserved and cultivated at the experimental field of the NIHHS, RDA, Chungbuk Province, Korea. These samples were deposited at Korean medicinal herbarium in NIHHS (Table 1).

성능/효과

A summary of the 454 sequencing data for ginseng samples is presented in Table 2. As a result of pyrosequencing, 1,223,017 raw reads were generated, including 297,170 reads for Cheonryang, 305,673 for Yunpoong, 311,861 for the G03080 breeding line, and 308,313 for P. quinquefolius. The total and mean lengths of the reads were 156,420,089 bp and 441 bp for Cheonryang, 161,956,527 bp and 435 bp for Yunpoong, 165,070,255 bp and 451 bp for G03080, and 166,489, 892 bp and 460 bp for P.
The Dhn 5, 6, and 8 genes were small in number or there were no unigenes; therefore, there was a limited number of unigenes to compare with limited expression. Finally, the Dhn 7 gene had 537, 510, 209, and 50 unigenes in Cheonryang, G03080, Yunpoong and P. quinquefolius, respeEctively, whereas Cheonryang and G03080 showed relatively higher (2.5 times) expression compared to that in the other samples.
The results of functional classification using GO analysis confirmed that G03080 contained unigenes that respond to external stress and repair damaged DNA. Unigenes were also found in Cheonryang and were associated with ion binding involved in the homeostasis within cells and detoxification.
The translation results of the reference unigenes showed that there were 40,510 cases in which the longest sequence included both a start and an end codon, and 16,762 cases included either a start or an end codon. The results of annotating the reference unigenes from the phytozome database (http://www.
(2006) who presented results of experiments by comparing the extent of expression of Dhn genes with cold stress and abscisic acid treatment. Their results confirmed that there are nine Dhn genes expressed in P. ginseng, among which Dhn 9 is a unique gene expressed only in seeds. In particular, the Dhn 1, 6, and 7 genes are expressed when seeds are exposed to = 5C for > 10 hours.

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