Kean-Jin Lim

Turku Centre for Biotechnology
Supervisor: Stephen Rudd
Funding: other
Date: 31/10/2007

Application of comparative plant transcriptomics to model systematic plant genome evolution

The plant kingdom is amazingly rich in biodiversity. Within the approximately 1,000 million years of evolution since their last universal ancestor, a broad range of plant life has evolved with as many as 200,000 extant species available for comparative genomics. The underlying evolutionary signal from broad systematic comparative genomics studies within distinct lineages of plants will reveal the mechanisms by which plants have conquered land, their ecological niches and the biology of trait evolution. In order to establish comparative genomics we need the fullest range of complete plant genomes. However, this is an ideal that is currently disallowed by existing sequencing technologies and the often massively expanded plant genomes. But, by sampling from lower quality (and incomplete) cDNA collections from nodal species we can still compare and contrast their gene content and can compare the changes between evolutionary lineages. Bioinformatics methods can be used, and are absolutely essential, to interlace the webs of related proteins, and phylogenomic character can be derived amongst the diverse sequence collections. Our ability to perform comparative plant genomics using EST data alone is currently troubled by the unevenly distributed coverage of sequences across the plant kingdom. The bulk of ESTs are currently assigned to the higher plant (angiosperms) but few of the crucial evolutionary groups of the lower plants for example ferns, lycophytes, hornworts and charophytes have been adequately sampled. This studies proposal is a plant genomics project which combines methods from molecular biology and bioinformatics disciplines. We propose to perform shallow EST sequencing (as many as 10,000 sequence reads) from three distinct and nodal plant species (a fern, a lycophytes and perhaps a hornwort). Using the latest available techniques for assessing comparative genomics, we will look for candidate groups of proteins and distinct protein architectures that can be used to hypothesise the groups of proteins may be responsible for the evolution of taxonomically distinguishing morphological features. The result will kept in databases of orthologous plant proteins and a rich online resource for functional and comparative genomics. This will form a foundation for further research into the more "exotic" plant genomes.