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. 2018 Feb 9;8(1):2749.
doi: 10.1038/s41598-017-18782-0.

SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants

Gaurav Sablok  1 , Regan J Hayward  2 , Peter A Davey  2 , Rosiane P Santos  3 , Martin Schliep  2 , Anthony Larkum  2 , Mathieu Pernice  2 , Rudy Dolferus  4 , Peter J Ralph  5
Affiliations

SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants

Gaurav Sablok et al. Sci Rep. .

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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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Contig binning across the assembled species in SeagrassDB.
Figure 2
Figure 2
(a) Venn diagram using VennPainter available from https://github.com/linguoliang/VennPainter shows the shared single copy orthologs across aquatic plant species; (b) showing the shared single copy orthologs across the Cymodoceaceae, Araceae and Hydrocharitaceae; and (c) showing the shared single copy orthologs across the Zosteracea, Posidoniceae and Araceae.
Figure 3
Figure 3
Browsing SeagrassDB.
Figure 4
Figure 4
(a) Shows the protein alignment of H+-ATPase; (b) and (c) shows the structural conservation of H+-ATPases across the land and aquatic plants.
Figure 5
Figure 5
Phylogenetic resolution of H+ ATPase across the evolutionary time scale.
See this image and copyright information in PMC

References

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