Developing DNA-barcodes for ecologically important eukaryotic microbes

Lead Research Organisation: The Natural History Museum
Department Name: Life Sciences

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

10 25 50

 
Description The main aims of this project were to develop a DNA barcoding database, and to identify potential DNA barcoding markers, for economically important ciliate protozoa. Eight regions of the nuclear and mitochondrial DNA were examined to check their suitability for barcoding . Initially the mitochondrial cox1 gene and the nuclear ITS1, ITS2, and hypervariable D2 region of LSU rDNA seemed to be promising candidates for species delineation, while the hypervariable V2 and V4 regions of SSU rDNA, D1 of LSU rDNA and 5.8S rDNA gene did not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences. Further analyses revealed that the most promising DNA barcoding gene markers for spirotrich ciliates are the D1-D2 region of the LSU rDNA, followed by the hypervariable V4 region of the SSU rDNA. In addition, a new automated method, namely "Guided Phylogenomic Search in trees (GPSit)", was developed in order to streamline the workflow and reduce the bioinformatics expertise required for phylogenomic analyses of ciliates. GPSit should facilitate future analyses of additional gene markers based on phylogenomic data. GPSit should be also be applicable to any group of organisms.
Exploitation Route The database of 270 sequences of 120 species/populations of spirotrich ciliates has been uploaded onto the NCBI GenBank database. It is therefore publicly available.can thus be used and built upon for future research. The newly developed method for phylogenomic analysis (GPSit) should be applicable for any organism group.

The ability to identify protozoa in agroecosystems subject to ongoing change will allow monitoring of the environmental impact of these changes and the health of the ecosystems and capacity to deliver essential services.
Sectors Agriculture, Food and Drink,Environment

 
Description Royal Society International Exchanges Cost Share scheme with Natural Foundation of Science China (NFSC)
Amount £24,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 04/2014 
End 03/2016
 
Title Ciliate Barcoding Database 
Description We are developing a Ciliate barcoding database. SSU rDNA, ITS1-5.8s rDNA-ITS2, and LSU rDNA are amplified for 60 populations of Euplotes-complexand 178 new sequences added to the barcoding database of this group. Barcoding gaps for species discrimination ITS1-5.8s rDNA-ITS2 and LSU rDNA are amplified for 91 populations of oligotrichour species and 207 new sequences added to the database of this group. Barcoding gaps for species discrimination have been assessed for these markers. (3) Oligotrichous specific primers have been designed for amplifying D1-D2 region of LSU rDNA, and they are used to detect related OTUs in 7 sites along Pearl River. (4) Meta-barcoding of Spirotrichea is on-going in 58 water samples from Pearl River and South China Sea. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact The database is still being constructed and is not yet ready to share. 
 
Title GPSit: An Automated Method for Evolutionary Analysis of Nonculturable Ciliated Microeukaryotes 
Description "Guided Phylogenomic Search in trees" (GPSit) is an automated method for phylogenomic analysis which starts from predicted protein sequences of newly sequenced species and a well-defined customized orthologous database. Although designed for microeukaryotes (and ciliates in particular), it could be applied to any organism group. 
Type Of Material Data analysis technique 
Year Produced 2018 
Provided To Others? Yes  
Impact The paper describing GPSit is still in press at the time of writing so the impact of this method has yet to happen 
 
Description OUC 
Organisation Ocean University of China
Country China 
Sector Academic/University 
PI Contribution Expertise in project planning, some aspects of data analysis, and dissemination of results.
Collaborator Contribution Access to OUC Ciliate DNA Bank, data generation, some aspects of data analysis, and dissemination of results.
Impact Eight jointly authored papers published in international peer-reviewed journals and presentations at two international conferences.
 
Description SCNU 
Organisation South China Normal University
Country China 
Sector Academic/University 
PI Contribution The NHM contributed expertise in project planning, aspects of data analysis, training, dissemination of results, and report writing
Collaborator Contribution The SCNU contributed consumables, access to equipment, fieldwork, generation of data and aspects of data analysis.
Impact Ten jointly authored papers published in international peer-reviewed journals and several oral and poster presentations at national and international conferences as a direct result of the award. Numerous (ca. 30) jointly authored papers have been published, and presentations at several conferences have been given, in the ca. 10 years of collaboration between the SCNU and NHM.
Start Year 2007
 
Description XJU 
Organisation Xi'an Jiaotong University
Country China 
Sector Academic/University 
PI Contribution Expertise in project planning, some aspects of data analysis, training, dissemination of results and report writing.
Collaborator Contribution Provision of consumables, use of equipment, fieldwork, generation of data, some aspects of data analysis and dissemination of results.
Impact Four jointly authored papers published in international peer-reviewed journals generated as a direct result of the award. At least ten other papers published as a result of previous collaboration.
Start Year 2009
 
Description Oral Presentations on Ciliate Barcoding 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Two oral presentations were given at International Conferences in China, disseminating information about the project to potentially interested researchers.
Year(s) Of Engagement Activity 2014,2015
 
Description Poster presentations on Ciliate Barcoding 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentations were made at international conferences in the UK (2014) and China (2015) to disseminate information about the work to attending scientists leading to several discussions with interested researchers and students.
Year(s) Of Engagement Activity 2014,2015