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

Sablok, Gaurav; Hayward, Regan J.; Davey, Peter A.; Santos, Rosiane P.; Schliep, Martin; Larkum, Anthony W. D.; Pernice, Mathieu; Ralph, Peter J.

doi:10.1038/s41598-017-18782-0

Cited by 12 publications

(9 citation statements)

References 50 publications

(76 reference statements)

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“…Next-generation DNA sequencing combined with bioinformatics (Taberlet et al, 2012) will help diminish taxonomic bias such as sequencing old herbarium specimens of very rare species such as Halodule bermudensis. The rapid growth of large databases such as GenBank, 6 SeagrassDB (Sablok et al, 2018), and Treebase, 7 allows researchers to download available phylogenies or DNA sequences to build their own (Morell, 1996;Piel et al, 2000;Page, 2007). Taxonomic bias can also be reduced by targeting future collecting in poorly sampled clades.…”

Section: Overcoming the Impedimentsmentioning

confidence: 99%

Impediments to Understanding Seagrasses’ Response to Global Change

Rock

Daru

2021

Front. Mar. Sci.

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Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass response from climate change. First, our knowledge of seagrass occurrence information is prevalent with biases, gaps and uncertainties that can influence inferences on species response to global change. Second, research on seagrass diversity has been focused on species-level metrics that can be measured with data from the present – but rarely accounting for the shared phylogenetic relationships and evolutionary distinctiveness of species despite species evolved and diversified from shared ancestors. Third, compared to the mass production of species occurrence records, computational tools that can analyze these datasets in a reasonable amount of time are almost non-existent or do not scale well in terms of computer time and memory. These impediments mean that scientists must work with incomplete information and often unrepresentative data to predict how seagrass diversity might change in the future. We discuss these shortfalls and provide a framework for overcoming the impediments and diminishing the knowledge gaps they generate.

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Section: Overcoming the Impedimentsmentioning

confidence: 99%

Impediments to Understanding Seagrasses’ Response to Global Change

Rock

Daru

2021

Front. Mar. Sci.

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“…These two publications gave insight into the molecular adaptation steps to marine environment and supported that severe changes in cell wall composition were necessary. Sablok et al (2018) provided access to a transcriptomics database called "SeagrassDB", which allows authors to perform comparative trancriptomics on eight seagrass species and other aquatic plant species. With the same idea Wissler et al (2009) implemented the "Dr. Zompo" database, which is focused on Z. marina and Posidonia oceanica.…”

Section: Information On Cell Wall Relevant Genesmentioning

confidence: 99%

The Cell Wall of Seagrasses: Fascinating, Peculiar and a Blank Canvas for Future Research

Pfeifer

Classen

2020

Front. Plant Sci.

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Seagrasses are a polyphyletic group of angiosperm plants, which evolved from early monocotyledonous land plants and returned to the marine environment around 140 million years ago. Today, seagrasses comprise the five families Zosteraceae, Hydrocharitaceae, Posidoniaceae, Cymodoceaceae, and Ruppiaceae and form important coastal ecosystems worldwide. Despite of this ecological importance, the existing literature on adaption of these angiosperms to the marine environment and especially their cell wall composition is limited up to now. A unique feature described for some seagrasses is the occurrence of polyanionic, low-methylated pectins mainly composed of galacturonic acid and apiose (apiogalacturonans). Furthermore, sulfated galactans have been detected in some species. Recently, arabinogalactan-proteins (AGPs), highly glycosylated proteins of the cell wall of land plants, have been isolated for the first time from a seagrass of the baltic sea. Obviously, seagrass cell walls are characterized by new combinations of structural polysaccharide and glycoprotein elements known from macroalgae and angiosperm land plants. In this review, current knowledge on cell walls of seagrasses is summarized and suggestions for future investigations are given.

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“…BUSCO and DOGMA both address the problem of quality assessment and can be used side-by-side (e.g. (15,16)). Both have some advantages depending on the data to be analyzed.…”

Section: Dogmamentioning

confidence: 99%

DOGMA: a web server for proteome and transcriptome quality assessment

Kemena

Dohmen

Bornberg‐Bauer

2019

Nucleic Acids Research

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Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment represents a crucial step prior to downstream analyses on novel transcriptomes and proteomes. DOGMA allows such a quality assessment to be carried out. The data of interest are evaluated based on a comparison with a core set of conserved protein domains and domain arrangements. Depending on the studied species, DOGMA offers precomputed core sets for different phylogenetic clades. We now developed a web server for the DOGMA software, offering a user-friendly, simple to use interface. Additionally, the server provides a graphical representation of the analysis results and their placement in comparison to publicly available data. The server is freely available under https://domainworld-services.uni-muenster.de/dogma/. Additionally, for large scale analyses the software can be downloaded free of charge from https://domainworld.uni-muenster.de.

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

Cited by 12 publications

References 50 publications

Impediments to Understanding Seagrasses’ Response to Global Change

Impediments to Understanding Seagrasses’ Response to Global Change

The Cell Wall of Seagrasses: Fascinating, Peculiar and a Blank Canvas for Future Research

DOGMA: a web server for proteome and transcriptome quality assessment

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