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2. First Contiguous Genome Assembly of Japanese Lady Bell (Adenophora triphylla) and Insights into Development of Different Leaf Types.

Author

Kang, Ji-Nam, Lee, Si-Myung, Choi, Ji-Weon, Lee, Seung-Sik, and Kim, Chang-Kug

Subjects
SAPONINS, LEAF development, GENOMES, GENE families, GENOME size, UNSATURATED fatty acids
Abstract

Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination even within the same species. Despite this, few studies have comprehensively characterized the development processes of different leaf types and triterpenoid saponin pathways in this plant. Herein, we provide the first report of a high-quality genome assembly of A. triphylla based on a combination of Oxford Nanopore Technologies and Illumina sequencing methods. Its genome size was estimated to be 2.6 Gb, and the assembled genome finalized as 2.48 Gb, containing 57,729 protein-coding genes. Genome completeness was assessed as 95.6% using the Benchmarking Universal Single-Copy Orthologs score. The evolutionary divergence of A. triphylla was investigated using the genomes of five plant species, including two other species in the Campanulaceae family. The species A. triphylla diverged approximately 51-118 million years ago from the other four plants, and 579 expanded/contracted gene families were clustered in the Gene Ontology terms. The expansion of the β-amyrin synthase (bAS) gene, a key enzyme in the triterpenoid saponin pathway, was identified in the A. triphylla genome. Furthermore, transcriptome analysis of the two leaf types revealed differences in the activity of starch, sucrose, unsaturated fatty acid pathways, and oxidoreductase enzymes. The heat and endoplasmic reticulum pathways related to plant stress were active in the development of round type leaf, while an enhancement of pyrimidine metabolism related to cell development was confirmed in the development of the linear type leaf. This study provides insight into the evolution of bAS genes and the development of different leaf types in A. triphylla. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

Author

Kim, Chang-Kug, primary, Seol, Young-Joo, additional, Perumal, Sampath, additional, Lee, Jonghoon, additional, Waminal, Nomar Espinosa, additional, Jayakodi, Murukarthick, additional, Lee, Sang-Choon, additional, Jin, Seungwoo, additional, Choi, Beom-Soon, additional, Yu, Yeisoo, additional, Ko, Ho-Cheol, additional, Choi, Ji-Weon, additional, Ryu, Kyoung-Yul, additional, Sohn, Seong-Han, additional, Parkin, Isobel, additional, and Yang, Tae-Jin, additional

Published
2018
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32. Short-term pretreatment with high CO2alters organic acids and improves cherry tomato quality during storage

Author

Sangwanangkul, Peerapong, Bae, Yeoung-Seuk, Lee, Jung-Soo, Choi, Hyun-Jin, Choi, Ji-Weon, and Park, Me-Hea

Abstract

Cherry tomatoes (Lycopersicon esculentum Mill.) are typically harvested when mature for best flavor, but they have a short shelf life. A short-term pretreatment with high CO2levels was investigated for its effect on prolonging shelf life and improving flavor. Mature red fruits treated with 20% or 60% CO2initially had significantly higher respiration after 3 hours of treatment compared to a control; respiration then declined to normal levels during storage. Fruits treated with CO2produced significantly less ethylene than the control on the day of treatment. High CO2treatments had no significant effect on firmness and fruit color. Fruits treated with 20% CO2had a lower decay rate than the control; however, high temperature and the 60% CO2treatment induced decay. Fruits treated with 20% CO2and stored at 12°C for 10-15 days tended to have the highest levels of titratable acidity and the lowest pH. In addition, individual organic acid contents of cherry tomatoes were altered after CO2treatment. High CO2treatments significantly increased tartaric acid levels during storage at 12°C or 20°C for 10 or 15 days, respectively. Citric acid content was lower at the end of the storage period, but fruits treated with 60% CO2still had relatively high levels when fruits were stored at 12°C. Malic and oxalic acid contents showed little response to high CO2treatments. Fumaric acid content significantly increased and was associated with severe deterioration at the end of storage at 20°C. These results suggest that a 20% CO2treatment with storage at 12°C can reduce deterioration of cherry tomatoes by altering organic acid content.

Published
2017
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36. A Multi-Layered Screening Method to Identify Plant Regulatory Genes.

Author

Kim, Chang-Kug, Kim, Jin-A, Choi, Ji-Weon, Jeong, In-Seon, Moon, Yi-Seul, Park, Dong-Suk, Seol, Young-Joo, Kim, Yong-Kab, Kim, Yong-Hwan, and Kim, Yeon-Ki

Abstract

We used a seven-step process to identify genes involved in glucosinolate biosynthesis and metabolism in the Chinese cabbage (Brassica rapa). We constructed an annotated data set with 34,570 unigenes from B. rapa and predicted 11,526 glucosinolate-related candidate genes using expression profiles generated across nine stages of development on a 47k-gene microarray. Using our multi-layered screening method, we screened 392 transcription factors, 843 pathway genes, and 4,162 ortholog genes associated with glucosinolate-related biosynthesis. Finally, we identified five genes by comparison of the pathway-network genes including the transcription-factor genes and the ortholog-ontology genes. The five genes were anchored to the chromosomes of B. rapa to characterize their genetic-map positions, and phylogenetic reconstruction with homologous genes was performed. These anchored genes were verified by reverse-transcription polymerase chain reaction. While the five genes identified by our multi-layered screen require further characterization and validation, our study demonstrates the power of multi-layered screening after initial identification of genes on microarrays. [ABSTRACT FROM PUBLISHER]

Published
2014
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37. First Contiguous Genome Assembly of Japanese Lady Bell ( Adenophora triphylla ) and Insights into Development of Different Leaf Types.

Author

Kang JN, Lee SM, Choi JW, Lee SS, and Kim CK

Subjects
Humans, Japan, Asia, Eastern, Campanulaceae, Triterpenes, Saponins
Abstract

Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination even within the same species. Despite this, few studies have comprehensively characterized the development processes of different leaf types and triterpenoid saponin pathways in this plant. Herein, we provide the first report of a high-quality genome assembly of A. triphylla based on a combination of Oxford Nanopore Technologies and Illumina sequencing methods. Its genome size was estimated to be 2.6 Gb, and the assembled genome finalized as 2.48 Gb, containing 57,729 protein-coding genes. Genome completeness was assessed as 95.6% using the Benchmarking Universal Single-Copy Orthologs score. The evolutionary divergence of A. triphylla was investigated using the genomes of five plant species, including two other species in the Campanulaceae family. The species A. triphylla diverged approximately 51-118 million years ago from the other four plants, and 579 expanded/contracted gene families were clustered in the Gene Ontology terms. The expansion of the β-amyrin synthase ( bAS ) gene, a key enzyme in the triterpenoid saponin pathway, was identified in the A. triphylla genome. Furthermore, transcriptome analysis of the two leaf types revealed differences in the activity of starch, sucrose, unsaturated fatty acid pathways, and oxidoreductase enzymes. The heat and endoplasmic reticulum pathways related to plant stress were active in the development of round type leaf, while an enhancement of pyrimidine metabolism related to cell development was confirmed in the development of the linear type leaf. This study provides insight into the evolution of bAS genes and the development of different leaf types in A. triphylla .

Published
2023
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