SeagrassDB: An Open-source Transcriptomics Landscape for Phylogenetically Profiled Seagrasses and Aquatic Plants

Overview

Journal Sci Rep

Specialty Science

Date 2018 Feb 11

PMID 29426939

Citations 5

Authors

Gaurav Sablok

Regan J Hayward

Peter A Davey

Rosiane P Santos

Martin Schliep

Anthony Larkum

Mathieu Pernice

Rudy Dolferus

Peter J Ralph

Affiliations

Soon will be listed here.

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 .

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