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. 2020 Dec 31:2020:baaa114.
doi: 10.1093/database/baaa114.

CorkOakDB-The Cork Oak Genome Database Portal

Cirenia Arias-Baldrich  1   2 , Marta Contreiras Silva  3 , Filippo Bergeretti  3 , Inês Chaves  3   4 , Célia Miguel  4   5 , Nelson J M Saibo  3 , Daniel Sobral  1   6 , Daniel Faria  1   7 , Pedro M Barros  3
Affiliations

CorkOakDB-The Cork Oak Genome Database Portal

Cirenia Arias-Baldrich et al. Database (Oxford). .

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/.

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Figures

Figure 1.
Figure 1.
Summary of the new features added to the structural annotation file from the Q. suber genome publication for the CorkOakDB, which are identified with ‘+’.
Figure 2.
Figure 2.
Distribution of cork oak publicly available NCBI BioSamples related to RNA-Seq data sets, according to cork oak tissue or organ.
Figure 3.
Figure 3.
View of Transcript Search page in CorkOakDB.
Figure 4.
Figure 4.
View of InterPro and Gene Ontology annotations for polypeptide sequence XP_023870408.1, obtained by selecting the ‘Annotations’ tab in the CorkOakDB.
Figure 5.
Figure 5.
View of significant blastx hits for mRNA sequence XM_024066098.1, obtained by selecting the ‘BLAST results’ tab.
Figure 6.
Figure 6.
BLAST results for blastp search of the Arabidopsis MYB39 transcription factor on the cork oak protein database displayed in CorkOakDB.
Figure 7.
Figure 7.
Genome browser view of LOC112033310 structural annotation. RNA-seq data from three different tissues were selected to showcase exon coverage.
Figure 8.
Figure 8.
Gene expression analysis for the cork oak MYB39 (LOC112034724) and MYB92 (LOC112033310) orthologues, and two closely related MYB genes (LOC112030452 and LOC112006609) in different BioSamples included in BioProjects PRJEB3237 (A) and PRJEB33874 (B). These BioProjects were selected since they represent different cork oak tissues. BioSamples ERS168264, ERS168263 (upper panel), and ERX3494734 to ERX3494739 were obtained from developing phellem (or cork). BioSample names are hyperlinks to retrieve corresponding metadata.
Figure 9.
Figure 9.
Polypeptide feature page for XP_023921866 polypeptide. Using the Relationship tab, the correspondent Gene and Transcript IDs can be retrieved.
Figure 10.
Figure 10.
Phylogenetic analysis of selected cork oak and Arabidopsis MYBs TFs related to AtMYB39 and AtMYB92. Amino acid sequences were retrieved from CorkOakDB and TAIR, and multiple alignment of conserved MYB domains was performed using MAFFT v7. Phylogenetic inference was obtained using the Maximum Likelihood method with RAxML v8.2.12. Branch support was obtained by bootstrap analysis (1000 replications) and indicated for specific nodes (bootstrap value >50%).
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References

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