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http://dx.doi.org/10.5762/KAIS.2018.19.1.537

Transcriptomic Profile Analysis of Jeju Buckwheat using RNA-Seq Data  

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)
Publication Information
Journal of the Korea Academia-Industrial cooperation Society / v.19, no.1, 2018 , pp. 537-545 More about this Journal
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.
Keywords
Buckwheat; Fagopyrum esculentum; Fagopyrum tataricum; RNA-seq; Transcriptome assembly;
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