Loading content, please wait..
loading..
Logo
Version 3.21
or
Publication Type J
Authors Sablok, G; Hayward, RJ; Davey, PA; Santos, RP; Schliep, M; Larkum, A; Pernice, M; Dolferus, R; Ralph, PJ
Author Full Name Sablok, Gaurav; Hayward, Regan J.; Davey, Peter A.; Santos, Rosiane P.; Schliep, Martin; Larkum, Anthony; Pernice, Mathieu; Dolferus, Rudy; Ralph, Peter J.
Title SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants
Source SCIENTIFIC REPORTS
Language English
Document Type Article
Keywords Plus ZOSTERA-MARINA; RNA-SEQ; POSIDONIA-OCEANICA; CYMODOCEA-NODOSA; PLASMA-MEMBRANE; GENE-EXPRESSION; GENOME; ARABIDOPSIS; PROTEIN; ACTIVATION
Abstract Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.
Author Address [Sablok, Gaurav; Hayward, Regan J.; Davey, Peter A.; Schliep, Martin; Larkum, Anthony; Pernice, Mathieu; Ralph, Peter J.] Univ Technol Sydney, C3, POB 123, Broadway, NSW 2007, Australia; [Santos, Rosiane P.] Univ Fed Sao Joao Del Rei, Lab Recursos Genet, Campus CTAN, BR-36307352 Sao Joao Del Rei, MG, Brazil; [Dolferus, Rudy] CSIRO Agr & Food, GPO Box 1700, Canberra, ACT 2601, Australia
Reprint Address Sablok, G; Ralph, PJ (reprint author), Univ Technol Sydney, C3, POB 123, Broadway, NSW 2007, Australia.
E-mail Address sablokg@gmail.com; Peter.Ralph@uts.edu.au
ResearcherID Number Ralph, Peter/C-5029-2009
ORCID Number Ralph, Peter/0000-0002-3103-7346; Pernice, Mathieu/0000-0002-3431-2104; Hayward, Regan/0000-0002-6300-3271; de Paula Santos, Rosiane/0000-0003-3233-6863
Funding Agency and Grant Number Science without Borders-CNPq, international exchange program of the Brazilian government; Australian Government; [2226018]
Funding Text GS acknowledges Internal Grant Number 2226018 for providing financial and computational support for this project. GS acknowledges the computational facilities provided by the Climate Change Cluster (C3) and National eResearch Collaboration Tools and Resources (NeCTAR) for hosting the database. RPS also acknowledges Science without Borders-CNPq, international exchange program of the Brazilian government for the scholarship program. This research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government.
Cited Reference Count 52
Times Cited 1
Total Times Cited Count (WoS, BCI, and CSCD) 1
Publisher NATURE PUBLISHING GROUP
Publisher City LONDON
Publisher Address MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
ISSN 2045-2322
29-Character Source Abbreviation SCI REP-UK
ISO Source Abbreviation Sci Rep
Publication Date FEB 9
Year Published 2018
Volume 8
Article Number 2749
Digital Object Identifier (DOI) 10.1038/s41598-017-18782-0
Page Count 10
Web of Science Category Multidisciplinary Sciences
Subject Category Science & Technology - Other Topics
Document Delivery Number FV5PG
Unique Article Identifier WOS:000424634000003
Plants associated with this reference

LEGAL NOTICES — This website is protected by Copyright © The University of Sussex, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021. The eHALOPH database is protected by Database Right and Copyright © The University of Sussex and other contributors, 2006, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021. This database is based on an earlier work by James Aronson.
THIS WEBSITE AND THIS DATABASE ARE PROVIDED ON AN "AS IS" BASIS, AND YOU USE THEM AND RELY ON THEM AT YOUR OWN RISK.

Contact email: halophytes@sussex.ac.uk
Credits – Tim Flowers, Joaquim Santos, Moritz Jahns, Brian Warburton, Peter Reed