Developing DNA-barcodes for ecologically important eukaryotic microbes
Lead Research Organisation:
Natural History Museum
Department Name: Life Sciences
Abstract
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Publications
Chen X
(2017)
The diverse morphogenetic patterns in spirotrichs and philasterids: Researches based on five-year-projects supported by IRCN-BC and NSFC.
in European journal of protistology
Chen X
(2018)
GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes.
in Molecular ecology resources
Fan Y
(2016)
Redescription of two little-known urostyloid ciliates, Anteholosticharandani (Grolière, 1975) Berger, 2003 and A. antecirrata Berger, 2006 (Ciliophora, Urostylida).
in European journal of protistology
Gao F
(2016)
Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora).
in Molecular phylogenetics and evolution
Gao F
(2017)
Systematic studies on ciliates (Alveolata, Ciliophora) in China: Progress and achievements based on molecular information.
in European journal of protistology
Pan X
(2016)
Morphology and systematics of two freshwater urostylid ciliates, with description of a new species (Protista, Ciliophora, Hypotrichia).
in European journal of protistology
Wang J
(2016)
Morphology, ontogeny and molecular phylogeny of a novel saline soil ciliate, Urosomoida paragiliformis n. sp. (Ciliophora, Hypotrichia)
in European Journal of Protistology
| 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 | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2014 |
| 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 |