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Bolbase specifications

Information


Unique identifier OMICS_13092
Name Bolbase
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Documentation


Maintainer


  • person_outline Wei Hua

Publication for Bolbase

Bolbase citations

 (16)
library_books

Comparative genomic and transcriptomic analyses of Family 1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress responsive regulation

2018
Sci Rep
PMCID: 5789830
PMID: 29382843
DOI: 10.1038/s41598-018-19535-3

[…] ols/hmmer/) web server was used to retrieve the genes containing UDPGT (PF00201.17) domain with significant hits in all three Brassica species. The BRAD database (http://brassicadb.org/brad/) and the Bolbase database (http://ocri-genomics.org/bolbase) were used for gene syntenic analysis. Expression Array and RNA Sequencing data were obtained from the Gene Expression database with the following ac […]

library_books

IntroMap: a signal analysis based method for the detection of genomic introgressions

2017
BMC Genet
PMCID: 5716257
PMID: 29202713
DOI: 10.1186/s12863-017-0568-5

[…] egions between the published reference genomes for Brassica oleracea var. capitata and Brassica rapa var. Chiifu-401. The reference genomes, along with the known syntenic regions were downloaded from Bolbase and BRAD, respectively [, ]. A program was then developed in Python, and made available as part of the IntroMap package, to construct three simulated genomes. The simulated genomes are compris […]

library_books

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

2017
BMC Genomics
PMCID: 5683364
PMID: 29132315
DOI: 10.1186/s12864-017-4244-y

[…] re identified in the B. oleracea genome (i.e., BoCNGC1–26). Of the 26 BoCNGC genes identified in the latest genome assembly version in Ensembl Plants, 16 and 24 were detected in earlier versions from Bolbase (v.1.3) and GenBank (v.2.1) respectively (Table ). The physiological and biochemical properties of the 26 BoCNGC proteins were determined by computing different parameters, and are tabulated i […]

call_split

Chemopreventive glucosinolate accumulation in various broccoli and collard tissues: Microfluidic based targeted transcriptomics for by product valorization

2017
PLoS One
PMCID: 5612653
PMID: 28945821
DOI: 10.1371/journal.pone.0185112
call_split See protocol

[…] Primer Express software (Applied Biosystems, Foster City, CA, USA) from cDNA sequences annotated by previous publication []. These sequence data saved at http://www.OCRI-genomics.org and a database, Bolbase, were produced by the Brassica oleracea Genome Sequencing Consortium (BoGSC). The one exception to this were primers for AOP2, which were created from cDNA sequence obtained from NCBI (AY04442 […]

library_books

Splicing related genes are alternatively spliced upon changes in ambient temperatures in plants

2017
PLoS One
PMCID: 5336241
PMID: 28257507
DOI: 10.1371/journal.pone.0172950

[…] e mapped against the Arabidopsis thaliana genome version TAIR10 (www.arabidopsis.org) using TopHat []. B. oleracea reads were aligned against the B. oleracea genome version 1.0 (www.ocri-genomics.org/bolbase/index.html). Reference based full-length transcript isoform reconstruction was performed for each sample separately using Cufflinks []. Cuffmerge, which is part of the cufflinks package, was f […]

library_books

Overexpression of the Novel Arabidopsis Gene At5g02890 Alters Inflorescence Stem Wax Composition and Affects Phytohormone Homeostasis

2017
Front Plant Sci
PMCID: 5266714
PMID: 28184233
DOI: 10.3389/fpls.2017.00068

[…] ), The Arabidopsis Information Resource (TAIR, http://www.arabidopsis.org/), the Brassica Database (http://brassicadb.org/brad/), the Brassica oleracea Genomics Database (http://www.ocri-genomics.org/bolbase/index.html), the B. napus Genomics Database (http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_napus/), and the Rice Genome Annotation Database (http://rice.plantbiology.msu.edu/). In t […]


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Bolbase institution(s)
The Key Laboratory of Oil Crops Biology and Genetic Breeding, the Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, China; Institute of Vegetables and Flowers, the Chinese Academy of Agricultural Sciences, Beijing, China; Department of Agronomy, Purdue University, West Lafayette, IN, USA
Bolbase funding source(s)
This work was supported by grants from the Special Fund for Agro-scientific Research in the Public Interest (201103016), the National Basic Research Program of China (973 program, 2011CB109305), the National Natural Science Foundation of China (No. 31301039), the National High Technology Research and Development Program of China (863 Program, 2013AA102602), the Core Research Budget of the Non-profit Governmental Research Institution (No. 1610172011011), and the Hubei Agricultural Science and Technology Innovation Center of China.

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