LoniComp: a platform for gene function comparison and analysis between Lonicera japonica and Lonicera macranthoides

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Lonicera japonica and Lonicera macranthoides are vital medicinal plants.
• Recent chromosome-level genome assemblies offer new opportunities for gene function research.
• Existing tools like LjaFGD are outdated due to advancements in genomic and transcriptomic data.

Purpose of the Study:

• To develop an updated, comprehensive platform for comparative gene function analysis in Lonicera species.
• To integrate new genomic, transcriptomic, and functional annotation data.
• To provide enhanced tools for researchers studying Lonicera gene functions.

Main Methods:

• Construction of co-expression networks using chromosome-level genomic and transcriptomic data for L. japonica and L. macranthoides.
• Comprehensive gene annotation using NR, TAIR, Swissprot, and trEMBL databases.
• Functional prediction (GO, KEGG) and gene family identification using InterProScan, GhostKOALA, iTAK, HMMER, and InParanoid.
• Development of the LoniComp web platform (www.gzybioinformatics.cn/LoniComp) integrating these data and analyses.

Main Results:

• LoniComp provides integrated genomic and transcriptomic data with processed functional annotations for Lonicera species.
• The platform includes tools for sequence analysis (BLAST, Extract Sequence), functional enrichment, differential gene expression (DEG), and visualization (Heatmap, JBrowse2).
• Demonstrated utility of LoniComp with examples like LjFT and LjMYB12, showcasing its effectiveness for gene function studies.

Conclusions:

• LoniComp is a superior, information-rich alternative to LjaFGD for Lonicera gene function research.
• The platform facilitates comparative analysis and enhances the utilization of public genomic and transcriptomic resources.
• LoniComp empowers researchers with advanced tools for in-depth gene function studies in medicinal Lonicera species.