Wolfberry genome database: integrated genomic datasets for studying molecular biology

You-Long Cao; You-Yi Chen; Yan-Long Li; Chung-I Li; Shao-Ting Lin; Bing-Ru Lee; Chun-Lin Hsieh; Yu-Yun Hsiao; Yun-Fang Fan; Qing Luo; Jian-Hua Zhao; Yue Yin; Wei An; Zhi-Gang Shi; Chi-Nga Chow; Wen-Chi Chang; Chun-Lin Huang; Wei-Hung Chang; Zhong-Jian Liu; Wei-Sheng Wu; Wen-Chieh Tsai

doi:10.3389/fpls.2024.1310346

Wolfberry genome database: integrated genomic datasets for studying molecular biology

Front Plant Sci. 2024 Feb 20:15:1310346. doi: 10.3389/fpls.2024.1310346. eCollection 2024.

Authors

You-Long Cao^#^{1

2}, You-Yi Chen^#³, Yan-Long Li^#^{1

2}, Chung-I Li⁴, Shao-Ting Lin⁵, Bing-Ru Lee⁶, Chun-Lin Hsieh⁶, Yu-Yun Hsiao⁷, Yun-Fang Fan^{1

2}, Qing Luo^{1

2}, Jian-Hua Zhao^{1

2}, Yue Yin^{1

2}, Wei An^{1

2}, Zhi-Gang Shi^{1

2}, Chi-Nga Chow⁸, Wen-Chi Chang⁸, Chun-Lin Huang⁹, Wei-Hung Chang^{10

11}, Zhong-Jian Liu^{12

13

14}, Wei-Sheng Wu⁶, Wen-Chieh Tsai^{5

7

8

15

16}

Affiliations

¹ National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China.
² Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China.
³ Department of Agronomy, National Chiayi University, Chiaiyi, Taiwan.
⁴ Department of Statistics, National Cheng Kung University, Tainan, Taiwan.
⁵ Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan.
⁶ Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan.
⁷ Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
⁸ Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan.
⁹ Department of Biology, National Museum of Natural Science, Taichung, Taiwan.
¹⁰ Department of Psychiatry, National Cheng Kung University Hospital, Collage of Medicine, National Cheng Kung University, Tainan, Taiwan.
¹¹ Department of Psychiatry, National Cheng Kung University Hospital, Douliu, Taiwan.
¹² Key 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.
¹³ Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China.
¹⁴ Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China.
¹⁵ Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
¹⁶ University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.

^# Contributed equally.

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: Lycium barbarum; genomics; transcriptomics; user-friendly; wolfberry; wolfberry genome database (WGDB).

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Publication costs was funded by the Ministry of Science and Technology, Ningxia (NGSB-2021-2-01, 2021BEF02002-02), the Ministry of Science and Technology, Taiwan (MOST 111-2313-B-006-003-, MOST 110-2313-B-006-002-MY3, MOST 110-2622-B-006-009-, and MOST−111–2221−E−006–151−MY3), National Key R&D Program of China (Grant No. 2019YFD1000400), and National Natural Science Foundation of China [no. 31870199]. The funders have no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.