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<p><i>Lonicera japonica</i> and <i>L. macranthoides</i> are popular medicinal plants used for treating various diseases. Recently, new chromosome level genomes of <i>Lonicera</i> have provided a huge resource for understanding gene function. Although LjaFGD was created for analyzing <i>L. japonica</i> gene functions, it is now outdated due to updated genomes and more transcriptome data.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 <i>L. japonica</i> and <i>L. macranthoides</i>. 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 (<a href="http://www.gzybioinformatics.cn/LoniComp">www.gzybioinformatics.cn/LoniComp</a>) 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 <i>LjFT</i> and <i>LjMYB12</i>. It offers superior genomic data, transcriptomic resources<Emphasis Type="Underline">,</Emphasis> and analysis tools compared to LjaFGD, aiding researchers in gene function studies and comparison.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月1日

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  • Jingjie Zhang,
  • Bingbing Pan,
  • Jiangxin Yang,
  • Qi Pan,
  • Panpan Zhu,
  • Jiaotong Yang,
  • Mian Zhang,
  • Qiaoqiao Xiao

摘要

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 Although LjaFGD was created for analyzing L. japonica gene functions, it is now outdated due to updated genomes and more transcriptome data.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.