PhD Fellowship:
Sugarcane Phylogenomics
Phylogenomics and
and Bioinformatics
The South African Sugarcane Research Institute (SASRI) is a division of the South African Sugar Association and is
funded by the South African sugar industry. The institute has a complement of 45 professional scientists who
engage in a diversity of multi-disciplinary sugarcane research projects, the scope of which ranges across
bioinformatics, genomics, breeding, crop modelling, molecular pathology and physiology. SASRI is actively engaged
in sugarcane genomics and bioinformatics research and the Doctoral research fellow will play a pivotal role in
sugarcane molecular phylogenomics.

The Project:
The aim of the project is to conduct molecular phylogenomic analyses amongst Saccharum and related species
based on whole chloroplast genomes. The information and knowledge gathered by the project will provide
additional direction to the industrys introgression/diversification breeding initiatives.

Specific objectives are:
To assemble 75 chloroplast genomes sequenced by SASRI by mapping to an in-house assembled reference.
To fully annotate by remapping against assembled reference chloroplasts.
To identify and download representative whole genome grass sequences from the NCBI database.
To conduct de novo assembly and annotation of chloroplast sequences from NCBI datasets.
To perform molecular phylogenomic analyses on all the assembled chloroplast genomes.
To identify SNPs as a means of discriminating between closely related varieties/genotypes.
To create chloroplast region barcode to identify minimum number of regions required to phylogenetically
discriminate species and varieties.
To develop new tools for annotation and assembly

The PhD Candidate: Desirable and Essential Characteristics
Essential Characteristics

Desirable Characteristics

An undergraduate qualification in physical/
mathematical/biological sciences, with a Masters in
bioinformatics/ biological sciences (with
programming element) and/or software
development discipline.
Proficiency in PERL , JAVA or PYTHON
Interest and willingness to transition in to the field
of computational biology.
Written and verbal fluency in English.
Excellent organisational skills.
Ability to interact with and work in multidisciplinary teams.

Experience in:
the analyses of complex data structures; preferably
in the area of genomics;
Phylogenetics or graph theory
UNIX and shell scripting

The PhD research project will provide
useful experience for a computational
biologist or a physical/computer
scientists, wishing to transition into

Additional Information
The successful applicant will be provided with a competitive bursary, which will be renewable annually for a
period of three years.
Comfortable and secure housing will be provided on-site at the institute.
For further information, please email [email protected]
Curriculum vitae along with details of relevant experience and covering letters of
application may be emailed to: Zama Khoza at the address above.

The South
South African
African Sugarcane
Sugarcane Research
Research Institute
Institute is
is a

Further information
African African
may be
accessed on

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