Seagrass database launched
- UTS researchers in The Plant Functional Biology and Climate Change Cluster (C3) are investigating some of the complex scientific questions around seagrass biology and physiology to improve environmental management and policy outcomes.
- A new RNA sequencing (transcriptomics) open access database for Zostera muelleri has been launched as tool for the broader seagrass research community
- This is a first, current databases lack marine and Southern Hemisphere species for comparison
Australia has the largest diversity of seagrass species in the world and a large area, approximately 50,000 km2 of seagrass meadows, in shallow subtidal and intertidal environments around the country.
Seagrasses not only play a vital role in the healthy functioning of coastal wetlands they also mitigate against climate change by locking up large amounts of carbon in their sediments, roots and leaves. Unfortunately, seagrass habitats worldwide are declining due to a range of environmental pressures and human-induced disturbances. The seagrass research community needs new tools to help protect these important ecosystems.
Recently, a team
"This new database is a key aspect of our new capacity at UTS to understand seagrass physiology. We are on the verge of an exciting new era of ‘molecular physiology’ that will revolutionise our understanding of how seagrass respond to human impacts, as well as the threats linked to climate change", said C3 Director Professor Peter Ralph.
C3’s environmental bioinformatician Dr Gaurav Sablok said that currently available databases not lacked marine species and didn’t contain any species from the Southern Hemisphere.
“Current portals tend to use land-based plant species as models for comparison. The development of ZosTDB, represents a significant breakthrough for Australian aquatic researchers, in particular it allows the comparisons with the flowering land plants and with the basal aquatic marine species Spirodela polyrihza,” he said.
Transcriptomics (RNA sequencing) allows scientists to identify the specific genes, and their attributes, responsible for particular biological and biochemical functions.
“This functional analysis at the molecular biology level helps define the ecological adaption of species and the genetic influence of key parameters,” explains C3 PhD candidate Peter Davey who contributed to the data analysis.
“In the case of Z muelleri, we want to know which genes help the plant adapt to changes in light, temperature and oxygen and carbon dioxide concentrations. This is because these are critical parameters for seagrass health and productivity and also those likely to be impacted by environmental stressors such as dredging, coastal runoff and climate change.”
Dr Sablok added that by presenting transcriptome wide Gene Ontologies, InterPro domains, simple sequence repeats (SSRs) and evolutionary conserved orthologs, "ZosTDB bridges the gap between the evolution and genic responses to these environmental disturbances".
C3 student Regan Hayward has contributed to the development of the portal as part of an Honours degree at UTS. He believes that one of the powerful aspects of the new portal, which uses C3 High Performance Computing and NCI-based NECTAR infrastructure, is its data visualisation capability and ease of use.
“The portal has the capacity for researchers to generate tables and graphs for comparative analysis. It aims to bridge the gap between bench scientists and next generation sequencing techniques in one easily accessible portal,” he said.
“Ultimately we want to be able to conserve local seagrass diversity so that impacted seagrass habitats can be restored more efficiently by identifying the genes that respond to climatic changes. We hope the seagrass research community will be able to use the portal to better understand the impacts of climate change on seagrass function and thus devise effective restoration strategies," he said.
Research Team details;
ZosTDB http://184.108.40.206/ presenting transcriptome wide Gene Ontologies, InterPro domains, simple sequence repeats (SSRs) and evolutionary