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

Wolfberry genome database: integrated genomic datasets for studying molecular biology

You-Long Cao #  1   2 , You-Yi Chen #  3 , Yan-Long Li #  1   2 , Chung-I Li  4 , Shao-Ting Lin  5 , Bing-Ru Lee  6 , Chun-Lin Hsieh  6 , Yu-Yun Hsiao  7 , 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 Chow  8 , Wen-Chi Chang  8 , Chun-Lin Huang  9 , Wei-Hung Chang  10   11 , Zhong-Jian Liu  12   13   14 , Wei-Sheng Wu  6 , Wen-Chieh Tsai  5   7   8   15   16
Affiliations

Wolfberry genome database: integrated genomic datasets for studying molecular biology

You-Long Cao et al. Front Plant Sci. .

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).

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Overview of Wolfberry Genome Database architecture.
Figure 2
Figure 2
Step-by-step guide for the Genome browser page.
Figure 3
Figure 3
Step-by-step guide for the Gene annotation page.
Figure 4
Figure 4
Step-by-step guide for the Transcriptome page.
Figure 5
Figure 5
Step-by-step guide for the Metabolism pathway page.
Figure 6
Figure 6
Step-by-step guide for the Tools Browse tools including Domain_Interpro, Domain_Pfam, and Domain_GO.
Figure 7
Figure 7
Step-by-step guide for the Tools_Browse tools including TF-Arabidopsis thaliana and TF-Oryza sativa.
Figure 8
Figure 8
Step-by-step guide for the Tools_Nucleotide BLAST page.
Figure 9
Figure 9
Step-by-step guide for the Tools_Protein BLAST page.
Figure 10
Figure 10
Step-by-step guide for the Tools_Domain search page.
Figure 11
Figure 11
Step-by-step guide for the Tools_GO search page.
Figure 12
Figure 12
Step-by-step guide for the Tools_Gene expression profile.
Figure 13
Figure 13
A Case study showing the analysis steps of WRKY transcri ption factor regulating the carotenoids biosynthesis.
See this image and copyright information in PMC

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