Journal of the Korea Academia-Industrial cooperation Society (한국산학기술학회논문지)

The Korea Academia-Industrial cooperation Society (한국산학기술학회)
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Transcriptomic Profile Analysis of Jeju Buckwheat using RNA-Seq Data

NA-Seq를 이용한 제주산 메밀의 발아초기 전사체 프로파일 분석

  • Han, Song-I (Subtropical/tropical Organism Gene Bank, Jeju National University) ;
  • Chung, Sung Jin (JeromBiomedicine Co.,ltd.) ;
  • Oh, Dae-Ju (Jeju Biodiversity Research Institute, Jeju Technopark) ;
  • Jung, Yong-Hwan (Jeju Biodiversity Research Institute, Jeju Technopark) ;
  • Kim, Chan-Shick (Faculty of Biotechnology, College of Applied Life Science, SARI, Jeju Naional University) ;
  • Kim, Jae-hoon (Subtropical/tropical Organism Gene Bank, Jeju National University)
  • 한송이 (제주대학교 아열대.열대생물유전자은행센터) ;
  • 정성진 ((주)제롬바이오메디슨) ;
  • 오대주 ((재)제주테크노파크 생물종다양성연구소) ;
  • 정용환 ((재)제주테크노파크 생물종다양성연구소) ;
  • 김찬식 (제주대학교 생명공학부) ;
  • 김재훈 (제주대학교 아열대.열대생물유전자은행센터)
  • Received : 2017.12.20
  • Accepted : 2018.01.05
  • Published : 2018.01.31
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Abstract

In this study, transcriptome analysis was conducted to collect various information from Fagopyrum esculentum and Fagopyrum tataricum during the early germination stage. Total RNA was extracted from the seeds and at 12, 24, and 36 hrs after germination of Jeju native Fagopyrum esculentum and Fagopyrum tataricum and sequenced using the Illumina Hiseq 2000 platform. Raw data analysis was conducted using the Dynamic Trim and Lengths ORT programs in the SolexaQA package, and assembly and annotation were performed. Based on RNA-seq raw data, we obtained 16.5 Gb and 16.2 Gb of transcriptome data corresponding to about 84.2% and 81.5% of raw data, respectively. De novo assembly and annotation revealed 43,494 representative transcripts corresponding to 47.5Mb. Among them, 23,165 sequences were shown to have similar sequences with annotation DB. Moreover, Gene Ontology (GO) analysis of buckwheat representative transcripts confirmed that the gene is involved in metabolic processes (49.49%) of biological processes, as well as cell function (46.12%) in metabolic process, and catalytic activity (80.43%) in molecular function In the case of gibberellin receptor GID1C, which is related to germination of seeds, the expression levels increased with time after germination in both F. esculentum and F. tataricum. The expression levels of gibberellin 20-oxidase 1 were increased within 12 hrs of gemination in F. esculentum but continuously until 36 hrs in F. tataricum. This buckwheat transcriptome profile analysis of the early germination stage will help to identify the mechanism causing functional and morphological differences between species.

본 연구에서는 메밀의 발아초기에 발현되는 전사체의 다양한 정보 수집을 위해 양절메밀과 대관 3-3호의 RNA를 추출하여 전사체 분석을 수행하였다. 제주산 양절메밀과 대관3-3호의 종자 및 발아 후 12, 24, 36시간별로 total RNA를 추출하고, llumina Hiseq 2000 플랫폼을 사용하여 시퀀싱 하였다. SolexaQA package의 DynamicTrim과 LengthsORT 프로그램으로 이용하여 raw 데이터 분석을 실시한 후, 어셈블리(assembly)와 annotation을 수행하였다. RNA-seq raw 데이터로부터 약 84.2%, 81.5%에 해당하는 16.5Gb, 16.2Gb의 transcriptome 데이터를 확보하였다. 47Mb에 해당하는 43,494개의 대표적인 전사체(representative transcripts)를 확보하였고, 그 중에서 annotation DB와 서열 유사도를 갖는 서열은 23,165개로 확인되었다. 메밀의 representative transcripts 유전자의 유전자 온톨로지(gene ontology) 분석결과, biological process는 metabolic process (49.49%)에서, cellular components는 cell (46.12%)에서, molecular function은 catalyltic activity (80.43%)에서 유전자가 많이 분포되어 있는 것을 확인하였다. 종자의 발아에 관련된 gibberellin receptor GID1C의 경우에는 양절메밀, 대관 3-3호의 발현양이 모두 시간이 지남에 따라 증가되는 것을 확인할 수 있었으며, gibberellin 20-oxidase1의 경우에는 양절메밀에서는 발아 후 12 시간이내에 증가되었으나, 대관 3-3호에서는 36시간까지 유전자 발현양 증가하는 것을 확인할 수 있었다. 이러한 제주산 메밀의 발아초기 단계별 전사체 분석 데이터는 종간의 기능적, 형태학적 차이를 일으키는 메커니즘 규명에 도움을 줄 것으로 사료된다.

Keywords

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