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PhD student

Department

Microbiology and Plant Pathology
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Research Profiles

Primary Supervisor
Fanus Venter

Co Supervisor
Martin Coetzee
Emma Steenkamp

I am interested in genomics and incorporating this into bacterial systematics. Previous definitions for defining species in bacteria have always been difficult to apply with numerous exceptions to the rule. This is because an appropriate species concept encompassing all the evolutionary forces shaping bacterial species, is lacking.

For my PhD research I will investigate how we define bacterial taxonomic ranks and the level of cohesiveness of these ranks. I will also attempt to obtain a better understanding of all the processes from a theoretical point of view that shape species boundaries and will try to develop an approach for defining bacterial species based on the evolution and adaptation of bacteria rather than apply preset cut-off values. I will also investigate how shared gene content may influence the unique genome content of different species and thus influence the evolution of these species.

Palmer M*, Steenkamp ET, Coetzee MPA, Coutinho TA, Venter SN. 2016. Genome based phylogenetic  analysis to investigate the relationships between the genera Erwinia, Pantoea and Tatumella. Third Meeting of Bergey’s International Society for Microbial Systematics, Pune, India, 12-15 September. (oral presentation)

 

Du Plessis M, Steenkamp ET, Coetzee MPA, Venter SN*. 2014. Phylo- and comparative genomics of the Pantoea core genome. Second Meeting of Bergey's International Society for Microbial Systematics, Edinburgh, Scotland, 7-10 April. (oral presentation)

 

Du Plessis M, Steenkamp ET, Coetzee MPA*, Venter SN. 2014. Phylo- and comparative genomics of the Pantoea core genome. 11th Conference of the Southern African Society for Systematic Biology, Hogsback, South Africa, 6-10 April. (oral presentation)

 

Du Plessis M*, Steenkamp ET, Coetzee MPA, Coutinho TA, Venter SN. 2013. The evolution of the Pantoea core genome. 18th Biennial Congress of the South African Society for Microbiology, Bela-Bela, South Africa, 24-27 November. (poster presentation)

 

Du Plessis M*, Steenkamp ET, Coutinho TA, Venter SN. 2012. The validation of genomic approaches for the delineation of species in the genus Pantoea. 10th Meeting of the Southern African Society for Systematic Biology, Arniston, South Africa, 16-19 July. (oral presentation)


Phylo- and comparative genomics Workshop. 2016. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by A Kanzi, M Palmer and W-Y Chan.

Advanced PhylogeneticsWorkshop. 2016. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Phylogenomics Workshop. 2015. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by M Palmer and W-Y Chan.

Advanced PhylogeneticsWorkshop. 2015. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Phylogenomics Workshop. 2014. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by M Palmer and Dr. AJ Potts.

Advanced PhylogeneticsWorkshop. 2014. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Seeing the network for the trees: Phylogenetic Networks Workshop. 2013. Kirstenbosch Research Centre, Cape Town, South Africa. Presented by Dr. GW Grimm and Dr. AJ Potts. (Attendee)

Advanced Phylogenetics Workshop. 2012. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Attendee)

 


Export to RIS
Publication
Beukes CW, Palmer M, Manyaka P, Chan W-Y, Avontuur JR, Van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers in Microbiology 8 10.3389/fmicb.2017.01154
Venter SN, Palmer M, Beukes CW, Chan W-Y, Shin G, Van Zyl E, Seale T, Coutinho TA, Steenkamp ET. (2017) Practically delineating bacterial species with genealogical concordance. Antonie van Leeuwenhoek 10.1007/s10482-017-0869-8
Palmer M, Steenkamp ET, Coetzee MPA, Chan W-Y, Van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits THM, Duffy B, Venter SN. (2017) Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek 10.1007/s10482-017-0852-4
Palmer M, De Maayer P, Poulsen M, Steenkamp ET, Van Zyl E, Coutinho TA, Venter SN. (2016) Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites. Standards in Genomic Sciences 11(23) 10.1186/s40793-016-0144-z PDF
Steenkamp ET, van Zyl E, Beukes CW, Avontuur J, Chan W-Y, Palmer M, Mthombeni LS, Phalane FL, Sereme TK, Venter SN. (2015) Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa. Systematic and Applied Microbiology 38(8):545-554. 10.1016/j.syapm.2015.09.003