Work

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

Year: 2025

Type: article

Abstract: Lonicera japonica and L. macranthoides are popular medicinal plants used for treating various diseases. Recently, new chromosome level genomes of Lonicera have provided a huge resource for understanding gene function. Although LjaFGD was created for analyzing L. japonica gene functions, it is now outdated due to updated genomes and more transcriptome data. Utilizing new chromosome-level genomic and transcriptomic data, we developed co-expression networks of L. japonica and L. macranthoides. Gene annotations were performed by comparing sequences with NR, TAIR, Swissprot, and trEMBL databases. GO and KEGG annotations were predicted using InterProScan and GhostKOALA software, while gene families were identified with iTAK, HMMER, and InParanoid. To fully leverage the utilization value of public resources and data, we developed LoniComp ( www.gzybioinformatics.cn/LoniComp ) as a newer and information-rich alternative, a platform for gene function comparison and analysis by integrating genomic, transcriptomic data and processed functional annotations. It features tools like BLAST, Extract Sequence, Enrichment, Heatmap, DEG, and JBrowse2. We demonstrated its use with examples like LjFT and LjMYB12. It offers superior genomic data, transcriptomic resources, and analysis tools compared to LjaFGD, aiding researchers in gene function studies and comparison.

Source: BMC Genomics

DOI: 10.1186/s12864-025-11507-y