Additional file 1 of Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species
Creators: name: Ichihara, Hisako
name: Yamada, Manabu
name: Kohara, Mitsuyo
name: Hirakawa, Hideki
name: Ghelfi, Andrea
name: Tamura, Takuro
name: Nakaya, Akihiro
name: Nakamura, Yasukazu
name: Shirasawa, Sachiko
name: Yamashita, Samatchaya
name: Toda, Yosuke
name: Harada, Daijiro
name: Fujishiro, Tsunakazu
name: Komaki, Akiko
name: Fawcett, Jeffrey A.
name: Sugihara, Eiji
name: Tabata, Satoshi
name: Isobe, Sachiko N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Information Systems
subject: FOS: Computer and information sciences

description: Additional file1: Supplementary Fig. S1. Structure of pages, the developed keyword search system. Blue and green boxes indicate external and developed search systems, respectively. Gray boxes indicate contents developed for the keyword search. Supplementary Fig. S2. Numbers of registered data in Plant GARDEN since 2019. The data is as of March every year. A) genome files, B) gene sequences, C) Marker. D) linkage map, E) trait related loci. Blue bars and pink lines indicate the annual registration number and cumulative number, respectively. Supplementary Fig. S3. A screen view of the assembled stats table on a genome sequence page of Lj3.0 in Lotus japonicus. We performed a test of the quality of the assembled genome and gene sequences by using BUSCOs. Supplementary Fig. S4. A screen view of the functional annotation in a gene sequence page, Lj3g3v0303780.2, on the Lj3.0 genome. Re annotation of all genes registered in Plant GARDEN was performed by our group using Hayai Annotation. A) A main gene table. B) A detailed table of the functional annotations displayed below the main table. The IDs shown in the detailed annotations table are linked to the external database. Supplementary Fig. S5. A screen view of base variant lists in japonicus A) A the variant call are described in the comments file. A and a text table, which show the variant bases with the letters A, G, T, and C, are available for download. The variant positions are displayed on the two browsers TASUKE + and JBrowse. B) A list of gvcf files and SRAs. The list is displayed by clicking the Line list button in the vcf file list. Supplementary Fig. S6. A screen view of the PCR based DNA marker lists. A) A partial view of the DNA marker list in Vitis vinifera. Marker names, types, and positions on the reference genome and the name of the reference genome are shown. B) The detailed information of the selected marker. The table is shown by clicking the marker ID in the marker list. The marker name, type, primer or target sequences and their positions on the genome, and source manuscript information are available. Allele information was derived from the source manuscript by manual curation. The restriction enzyme is for CAPS or dCAPS markers. Supplementary Fig. S7. A screen view of trait related loci lists in Brassicarapa A) Graphical view of registered locus positions of the reference genome. B) A part of the list of the registered trait related loci. The displayed information is changed by selecting the tabs. C) The detailed information of the selected locus. The table is shown by clicking the locus ID in the trait related loci list. The locus name, trait name, trait category, analysis method, population name, population type, position on the genome estimated via nearest markers, position on the linkage map (if available in the source manuscript), and source manuscript are shown in the table. Supplementary Fig. S8. BLAST analysis in Plant GARDEN. A) A screen view of BLAST analysis in the tablet version. B) The data flow of BLAST analysis in Plant GARDEN with the PC and tablet versions. Red and green represent the flow of OCR and BLAST, respectively.