Blast:We constructed a Blast database of L. japonica transcripts and protein sequences from which orthologous sequences of genes of interest in L. japonica can be obtained using the online Blast tool.

Cis-element Enrichment Analysis:We collected 1035 motifs to build a toolkit for motif enrichment analysis as previously description (Da et al., 2019; Wang et al., 2020; Yang et al., 2018; You et al., 2017; Zhang et al., 2015).

JBrowse:The JBrowse (Buels et al., 2016) tool for displaying omics data was introduced to display genome and transcriptome data.

Gene Sets Enrichment Analysis:Gene set enrichment analysis (GSEA)(Yi et al., 2013) is a method for annotating a gene set with unknown function using well-defined gene sets. Here we introduce a online GSEA tool to help users analysising gene functions.

Heatmap Analysis:Heatmap analysis tool of transcriptome samples were also constructed using highchart.js (

Yi, X., Du, Z., and Su, Z. (2013). PlantGSEA: a gene set enrichment analysis toolkit for plant community. Nucleic Acids Res 41: W98-103.
Da, L., Liu, Y., Yang, J., Tian, T., She, J., Ma, X., Xu, W., and Su, Z. (2019). AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. Front Plant Sci 10: 1333.
Wang, J., Ma, X., Yang, J., Hui, Y., She, J., Tian, T., Li, Z., Xu, W., Gao, Z., Su, Z., and Zhao, H. (2020). Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana). Frontiers in genetics 11: 378.
Yang, J., Liu, Y., Yan, H., Tian, T., You, Q., Zhang, L., Xu, W., and Su, Z. (2018). PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. Front Genet 9: 590.
You, Q., Xu, W., Zhang, K., Zhang, L., Yi, X., Yao, D., Wang, C., Zhang, X., Zhao, X., Provart, N.J., Li, F., and Su, Z. (2017). ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic acids research 45: 5625-5626.
Zhang, L., Guo, J., You, Q., Yi, X., Ling, Y., Xu, W., Hua, J., and Su, Z. (2015). GraP: platform for functional genomics analysis of Gossypium raimondii. Database : the journal of biological databases and curation 2015: bav047.