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| 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 |
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