Fig. 1

a Workflow of the CyDotian toolkit. b Comparison among CyDotian and other software or platforms. c Venn diagram of perfect repeat results identified by CyDotian versus perfect repeat results identified by repeat-match. d The starting screen of SAtoolkit, a toolkit that integrates three algorithms. e Evolutionary tree of life, paleopolyploidization, and number of LIR-containing genes in representative species of the plant kingdom, mainly horticultural plants. f Blast analysis of all LIR sequences in Arabidopsis thaliana, Brassica napus, Brassica rapa, and Brassica oleracea. g Statistical details of the number of element types that can be matched by all LIR in the four Cruciferae species. h Statistical details of the five duplication origins of the LIR-containing gene in four Cruciferae species. i Tissue expression of all LIR-containing and corresponding non-LIR-containing homologous gene pairs in Brassica rapa and Brassica oleracea. j Localization of the aspartate protease tandem repeat cluster gene containing AT2G28220 on the chromosome. k An evolutionary model for tandem duplication and gene fusion of the AT2G28220 gene in Arabidopsis thaliana. l Comparative dot plot results of two SARS-CoV-2 protein sequences. m Schematic diagram of the structure of the Type-1 PME amino acid. SP stands for signal peptide, TM stands for transmembrane domain, PMEI stands for pectin methylesterase inhibitor domain, PM stands for a processing motif (mainly RRLL or RKLL). n Comparison of the intragenic repeat density of the coding sequences of the pro-region and PME domain for all Type-1 PME genes in representative plants