더덕 및 씀바귀 참조전사체 단일 파일 DB 구축
Construction of a Single File Reference Transcriptome Database for Deodeok (Codonopsis lanceolata) and Sseumbagwi (Ixeridium dentata)
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
In this study, we constructed a reference transcriptome database for the special crops Codonopsis lanceolata (known as “deodeok”in Korean) and Ixeridium dentata (known as “sseumbagwi” in Korean). The reference transcriptome sequence based on PacBio Iso-Seq technologywas rapidly analyzed using various programs on a supercomputer at the Rural Development Administration to determine homologous genesearches, domain searches, and metabolic pathway-related information. Transcriptome information was organized into a single file database(DB) with a simple user interface using Microsoft Access, enabling efficient access and management of transcriptome sequences and functionalprediction information. The deodeok reference transcriptome DB included 49,677 transcriptome sequences, whereas the sseumbagwi referencetranscriptome DB included 73,757 transcriptome sequences. These reference transcriptome DBs can be utilized for various genomic analyses,such as gene discovery, gene expression analysis, inter-and intraspecies comparisons, and marker development, with particular potential foruse in secondary metabolite research. The reference transcriptome DBs constructed in this study are expected to contribute to enhancing theagricultural value and industrial applicability of deodeok and sseumbagwi
Abstract
In this study, we constructed a reference transcriptome database for the special crops Codonopsis lanceolata (known as “deodeok”in Korean) and Ixeridium dentata (known as “sseumbagwi” in Korean). The reference transcriptome sequence based on PacBio Iso-Seq technologywas rapidly analyzed using various programs on a supercomputer at the Rural Development Administration to determine homologous genesearches, domain searches, and metabolic pathway-related information. Transcriptome information was organized into a single file database(DB) with a simple user interface using Microsoft Access, enabling efficient access and management of transcriptome sequences and functionalprediction information. The deodeok reference transcriptome DB included 49,677 transcriptome sequences, whereas the sseumbagwi referencetranscriptome DB included 73,757 transcriptome sequences. These reference transcriptome DBs can be utilized for various genomic analyses,such as gene discovery, gene expression analysis, inter-and intraspecies comparisons, and marker development, with particular potential foruse in secondary metabolite research. The reference transcriptome DBs constructed in this study are expected to contribute to enhancing theagricultural value and industrial applicability of deodeok and sseumbagwi
참고문헌 (13)
- 배선화, "Identification of Interspecific and Intraspecific Single Nucleotide Polymorphisms in Papaver spp.", Plant Breeding and Biotechnology, 9(1), pp.55~64 (2021), 한국육종학회
- Buchfink B, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nat Methods, 18, pp.366~368 (2021)[DOI]
- Conesa A, "Blast2GO : a comprehensive suite for functional analysis in plant genomics", Int J Plant Genomics, 2008, pp.619832~ (2008)[DOI]
- Fu L, "CD-HIT : accelerated for clustering the next-generation sequencing data", Bioinformatics, 28, pp.3150~3152 (2012)
- "GitHub - TransDecoder/TransDecoder:TransDecoder source"[URL]
- Hossen MJ, "Codonopsis lanceolata : a review of its therapeutic potentials", Phytother Res, 30, pp.347~356 (2016)[DOI]
- 장우종, "A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform", Plant Breeding and Biotechnology, 5(1), pp.25~35 (2017), 한국육종학회[DOI]
- Jeon D, "Digitalizing breeding in plants : a new trend of next-generation breeding based on genomic prediction", Front Plant Sci, 14, pp.1092584~ (2023)[DOI]
- Jeong SY, "Codonopsis lanceolata water extract increases hepatic insulin sensitivity in rats with experimentally-induced type 2 diabetes", Nutrients, 9, pp.1200~ (2017)[DOI]
- Jones P, "InterProScan 5: genomescale protein function classification", Bioinformatics (Oxford, England), 30, pp.1236~1240 (2014)[DOI]
- 김인서, "Discrimination and Authentication of Eclipta prostrata and E. alba Based on the Complete Chloroplast Genomes", Plant Breeding and Biotechnology, 5(4), pp.334~343 (2017), 한국육종학회[DOI]
- Lim SS, "Effect of Aster scaber and Ixeris dentata on Contractility and Vasodilation of Cardiovascula and Endothelial Cell in Hyperlipidemic Rat", J Korean Soc Food Sci Nutr, 26, pp.300~307 (1997)
- Moriya Y, "KAAS : an automatic genome annotation and pathway reconstruction server", Nucleic Acids Res, 35(Suppl 2), pp.W182~W185 (2007)[DOI]