Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species

BMC Plant Biology

Database

Akihiro Nakaya¹  Mitsuyo Kohara²  Manabu Yamada²  Samatchaya Yamashita²  Hisako Ichihara²  Satoshi Tabata²  Hideki Hirakawa²  Akiko Komaki²  Sachiko Shirasawa²  Yosuke Toda²  Tsunakazu Fujishiro²  Sachiko N. Isobe²  Yasukazu Nakamura³  Andrea Ghelfi³  Daijiro Harada⁴  Jeffrey A. Fawcett⁵  Takuro Tamura⁶  Eiji Sugihara⁷ 

[1] Graduate School of Frontier Sciences, The University of Tokyo, 277-0882, Kashiwa, Chiba, Japan;Kazusa DNA Research Institute, 292-0813, Kisarazu, Chiba, Japan;Kazusa DNA Research Institute, 292-0813, Kisarazu, Chiba, Japan;Bioinformation and DDBJ Center, National Institute of Genetics, 411-8540, Mishima, Shizuoka, Japan;Kazusa DNA Research Institute, 292-0813, Kisarazu, Chiba, Japan;Present Address: Chitose Bio Evolution Pte. Ltd. Kawasaki, 213-0012, Kanagawa, Japan;Kazusa DNA Research Institute, 292-0813, Kisarazu, Chiba, Japan;Present Address: RIKEN iTHEMS, 351-0198, Wako, Saitama, Japan;Research and Development Center for Precision Medicine, University of Tsukuba, 305-8550, Tsukuba, Ibaraki, Japan;Research and Development Center for Precision Medicine, University of Tsukuba, 305-8550, Tsukuba, Ibaraki, Japan;Present Address: Division of Gene Regulation, Fujita Cancer Center, Research Promotion Headquarters, Fujita Health University School of Medicine, 470-1192, Toyoake, Aichi, Japan;

关键词: Database;    Plant;    Genome;    Gene;    Marker;    SNPs;    Cross-search;   

DOI  :  10.1186/s12870-023-04392-8

 received in 2022-07-12, accepted in 2023-07-18,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundPlant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species.Main bodyWe have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes.ConclusionThe aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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