Frontiers in Plant Science (Feb 2024)
Wolfberry genome database: integrated genomic datasets for studying molecular biology
- You-Long Cao,
- You-Long Cao,
- You-Yi Chen,
- Yan-Long Li,
- Yan-Long Li,
- Chung-I Li,
- Shao-Ting Lin,
- Bing-Ru Lee,
- Chun-Lin Hsieh,
- Yu-Yun Hsiao,
- Yun-Fang Fan,
- Yun-Fang Fan,
- Qing Luo,
- Qing Luo,
- Jian-Hua Zhao,
- Jian-Hua Zhao,
- Yue Yin,
- Yue Yin,
- Wei An,
- Wei An,
- Zhi-Gang Shi,
- Zhi-Gang Shi,
- Chi-Nga Chow,
- Wen-Chi Chang,
- Chun-Lin Huang,
- Wei-Hung Chang,
- Wei-Hung Chang,
- Zhong-Jian Liu,
- Zhong-Jian Liu,
- Zhong-Jian Liu,
- Wei-Sheng Wu,
- Wen-Chieh Tsai,
- Wen-Chieh Tsai,
- Wen-Chieh Tsai,
- Wen-Chieh Tsai,
- Wen-Chieh Tsai
Affiliations
- You-Long Cao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- You-Long Cao
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- You-Yi Chen
- Department of Agronomy, National Chiayi University, Chiaiyi, Taiwan
- Yan-Long Li
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Yan-Long Li
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan, Taiwan
- Shao-Ting Lin
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
- Bing-Ru Lee
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
- Chun-Lin Hsieh
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
- Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Yun-Fang Fan
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Yun-Fang Fan
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Qing Luo
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Qing Luo
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Jian-Hua Zhao
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Jian-Hua Zhao
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Yue Yin
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Yue Yin
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Wei An
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Wei An
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Zhi-Gang Shi
- National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Zhi-Gang Shi
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- Chi-Nga Chow
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
- Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
- Chun-Lin Huang
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Wei-Hung Chang
- 0Department of Psychiatry, National Cheng Kung University Hospital, Collage of Medicine, National Cheng Kung University, Tainan, Taiwan
- Wei-Hung Chang
- 1Department of Psychiatry, National Cheng Kung University Hospital, Douliu, Taiwan
- Zhong-Jian Liu
- 2Key Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization and International Orchid Research Center at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Zhong-Jian Liu
- 3Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
- Zhong-Jian Liu
- 4Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
- Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
- Wen-Chieh Tsai
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
- Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
- Wen-Chieh Tsai
- 5Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Wen-Chieh Tsai
- 6University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- DOI
- https://doi.org/10.3389/fpls.2024.1310346
- Journal volume & issue
-
Vol. 15
Abstract
Wolfberry, also known as goji berry or Lycium barbarum, is a highly valued fruit with significant health benefits and nutritional value. For more efficient and comprehensive usage of published L. barbarum genomic data, we established the Wolfberry database. The utility of the Wolfberry Genome Database (WGDB) is highlighted through the Genome browser, which enables the user to explore the L. barbarum genome, browse specific chromosomes, and access gene sequences. Gene annotation features provide comprehensive information about gene functions, locations, expression profiles, pathway involvement, protein domains, and regulatory transcription factors. The transcriptome feature allows the user to explore gene expression patterns using transcripts per kilobase million (TPM) and fragments per kilobase per million mapped reads (FPKM) metrics. The Metabolism pathway page provides insights into metabolic pathways and the involvement of the selected genes. In addition to the database content, we also introduce six analysis tools developed for the WGDB. These tools offer functionalities for gene function prediction, nucleotide and amino acid BLAST analysis, protein domain analysis, GO annotation, and gene expression pattern analysis. The WGDB is freely accessible at https://cosbi7.ee.ncku.edu.tw/Wolfberry/. Overall, WGDB serves as a valuable resource for researchers interested in the genomics and transcriptomics of L. barbarum. Its user-friendly web interface and comprehensive data facilitate the exploration of gene functions, regulatory mechanisms, and metabolic pathways, ultimately contributing to a deeper understanding of wolfberry and its potential applications in agronomy and nutrition.
Keywords
