Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.
Cross-search
Database
Gene
Genome
Marker
Plant
SNPs
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
12 Aug 2023
12 Aug 2023
Historique:
received:
12
07
2022
accepted:
18
07
2023
medline:
16
8
2023
pubmed:
12
8
2023
entrez:
11
8
2023
Statut:
epublish
Résumé
Plant 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. We 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. The 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.
Sections du résumé
BACKGROUND
BACKGROUND
Plant 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 BODY
METHODS
We 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.
CONCLUSION
CONCLUSIONS
The 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.
Identifiants
pubmed: 37568098
doi: 10.1186/s12870-023-04392-8
pii: 10.1186/s12870-023-04392-8
pmc: PMC10422841
doi:
Substances chimiques
Genetic Markers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
391Subventions
Organisme : Japan Science and Technology Agency
ID : the Database Integration Coordination Program
Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
Références
Bioinformatics. 2019 Nov 1;35(21):4427-4429
pubmed: 31093654
Methods Mol Biol. 2017;1533:1-31
pubmed: 27987162
Plant Physiol. 2002 Dec;130(4):1606-13
pubmed: 12481044
DNA Res. 2019 Dec 1;26(6):445-452
pubmed: 31539030
Breed Sci. 2014 Sep;64(3):264-71
pubmed: 25320561
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Genome Biol. 2016 Apr 12;17:66
pubmed: 27072794
Plant Cell Physiol. 2014 Jan;55(1):e8
pubmed: 24363285
BMC Plant Biol. 2009 Aug 22;9:112
pubmed: 19698131
Sci Rep. 2017 Feb 10;7:42338
pubmed: 28186158
Nucleic Acids Res. 2016 Jan 4;44(D1):D1181-8
pubmed: 26546515
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Microorganisms. 2019 Jun 13;7(6):
pubmed: 31200539
Nucleic Acids Res. 2008 Jan;36(Database issue):D991-8
pubmed: 17986457
Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
pubmed: 22110026
Nat Plants. 2021 Dec;7(12):1571-1578
pubmed: 34845350
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nucleic Acids Res. 2015 Jan;43(Database issue):D1036-41
pubmed: 25428362