Literature DB >> 33382885

CorkOakDB-The Cork Oak Genome Database Portal.

Cirenia Arias-Baldrich1,2, Marta Contreiras Silva3, Filippo Bergeretti3, Inês Chaves3,4, Célia Miguel4,5, Nelson J M Saibo3, Daniel Sobral1,6, Daniel Faria1,7, Pedro M Barros3.   

Abstract

Quercus suber (cork oak) is an evergreen tree native to the Mediterranean basin, which plays a key role in the ecology and economy of this area. Over the last decades, this species has gone through an observable decline, mostly due to environmental factors. Deciphering the mechanisms of cork oak's response to the environment and getting a deep insight into its biology are crucial to counteract biotic and abiotic stresses compromising the stability of a unique ecosystem. In the light of these setbacks, the publication of the genome in 2018 was a major step towards understanding the genetic make-up of this species. In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB). The CorkOakDB is supported by the BioData.pt e-infrastructure, the Portuguese ELIXIR node for biological data. The portal gives public access to search and explore the curated genomic and transcriptomic data on this species. Moreover, CorkOakDB provides a user-friendly interface and functional tools to help the research community take advantage of the increased accessibility to genomic information. A study case is provided to highlight the functionalities of the portal. CorkOakDB guarantees the update, curation and data collection, aiming to collect data besides the genetic/genomic information, in order to become the main repository in cork oak research. Database URL: http://corkoakdb.org/.
© The Author(s) 2020. Published by Oxford University Press.

Entities:  

Year:  2020        PMID: 33382885      PMCID: PMC7774466          DOI: 10.1093/database/baaa114

Source DB:  PubMed          Journal:  Database (Oxford)        ISSN: 1758-0463            Impact factor:   3.451


  19 in total

1.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

2.  GMAP: a genomic mapping and alignment program for mRNA and EST sequences.

Authors:  Thomas D Wu; Colin K Watanabe
Journal:  Bioinformatics       Date:  2005-02-22       Impact factor: 6.937

3.  SUBERMAN regulates developmental suberization of the Arabidopsis root endodermis.

Authors:  Hagai Cohen; Vadim Fedyuk; Chunhua Wang; Shuang Wu; Asaph Aharoni
Journal:  Plant J       Date:  2020-02-24       Impact factor: 6.417

4.  HISAT: a fast spliced aligner with low memory requirements.

Authors:  Daehwan Kim; Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2015-03-09       Impact factor: 28.547

5.  SGD: Saccharomyces Genome Database.

Authors:  J M Cherry; C Adler; C Ball; S A Chervitz; S S Dwight; E T Hester; Y Jia; G Juvik; T Roe; M Schroeder; S Weng; D Botstein
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

6.  Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak.

Authors:  Susana T Lopes; Daniel Sobral; Bruno Costa; Pedro Perdiguero; Inês Chaves; Augusta Costa; Célia M Miguel
Journal:  Tree Physiol       Date:  2020-02-20       Impact factor: 4.196

7.  BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.

Authors:  Tanya Barrett; Karen Clark; Robert Gevorgyan; Vyacheslav Gorelenkov; Eugene Gribov; Ilene Karsch-Mizrachi; Michael Kimelman; Kim D Pruitt; Sergei Resenchuk; Tatiana Tatusova; Eugene Yaschenko; James Ostell
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

8.  CottonGen: a genomics, genetics and breeding database for cotton research.

Authors:  Jing Yu; Sook Jung; Chun-Huai Cheng; Stephen P Ficklin; Taein Lee; Ping Zheng; Don Jones; Richard G Percy; Dorrie Main
Journal:  Nucleic Acids Res       Date:  2013-11-06       Impact factor: 16.971

9.  Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection.

Authors:  Rita Teresa Teixeira; Ana Margarida Fortes; Hua Bai; Carla Pinheiro; Helena Pereira
Journal:  Planta       Date:  2017-10-07       Impact factor: 4.116

10.  15 years of GDR: New data and functionality in the Genome Database for Rosaceae.

Authors:  Sook Jung; Taein Lee; Chun-Huai Cheng; Katheryn Buble; Ping Zheng; Jing Yu; Jodi Humann; Stephen P Ficklin; Ksenija Gasic; Kristin Scott; Morgan Frank; Sushan Ru; Heidi Hough; Kate Evans; Cameron Peace; Mercy Olmstead; Lisa W DeVetter; James McFerson; Michael Coe; Jill L Wegrzyn; Margaret E Staton; Albert G Abbott; Dorrie Main
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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