Doctoral defence in Biology - Sheeba Santhini Basil

Ph.D. student: Sheeba Santhini Basil

Dissertation title: Macromolecular characterization of the lichen Peltigera membranacea using nucleic acid sequencing & Identification of a new lichen species Peltigera islandica

Opponents: 
Dr. Imke Schmitt, Professor, Department of Ecology, Evolution and Biodiversity, Goethe University, Frankfurt, Germany.

Dr. Kristinn P. Magnússon, Professor of Molecular Genetics at the Faculty of Natural Resource Sciences, University of Akureyri.

Advisor: Dr. Ólafur S. Andrésson, Professor at the Faculty of Life and Environmental Sciences, University of Iceland.

Doctoral committee: 
Dr. Vivian P. W. Miao, Research Fellow at the Department of Microbiology and Immunology, University of British Columbia, Canada.
Dr. Zophonías O. Jónsson, Professor at the Faculty of Life and Environmental Sciences, University of Iceland.
Dr. Ólafur Héðinn Friðjónsson, Research group leader at Matís.

Chair of Ceremony: Dr. Anna Dóra Sæþórsdóttir, Professor at the Faculty of Life and Environmental Sciences, University of Iceland.

Abstract:
Lichens are a classic example of mutualism, where both partners benefit from each other. The mycobiont serves the photobiont by providing shelter, nutrients, and moisture from the environment and receives carbohydrates and sometimes fixed nitrogen from the photosynthetically active photobiont. Molecular analyses can provide insights into the mechanisms of mutual symbiosis in the cyanolichen Peltigera membranacea, but since the lichen is recalcitrant to culture, the global macromolecular components such as DNA, RNA, and proteins must be isolated from field samples. An annotated draft genome of the P. membranacea mycobiont is presented, accompanied by the analysis of tissue-specific transcriptomes and methylomes. The assembly consists of 3,033 scaffolds with a total genome size of ~43 Mbp, N50 of 34.52 kbp, and a G+C content of 44.4%. Transcriptomes were generated from about 43 million Illumina sequence reads obtained from three lichen tissues, apothecia, rhizines, and thallus, collected at three-time points. Using the Trinity assembler, initial de novo transcriptomes with a total of 110,092 transcript sequences were obtained with lengths ranging from 200 bases to 18,258 bases. Transcriptome data was incorporated into the AUGUSTUS software pipeline and was used to generate a draft annotation (P.mem v1.1) with 16,400 protein-coding models with gene descriptions, gene ontology terms, InterPro identifiers and EC (enzyme code) numbers. About 2,505 proteins were assigned to 112 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Eukaryotic core proteins were identified using BUSCO (Benchmarking Universal Single-Copy Orthologs), showing that the P. membranacea genome assembly (P.mem v1.1) represents 96.9% of the BUSCO genes. Furthermore, targeted protein-based searches identified key genes involved in symbiosis, DNA methylation, RNA–mediated silencing, the glyoxylate cycle, melanin pathways, sexual reproduction and nutrient assimilation, leading to a model for the flow of basic nutrients (carbon and nitrogen). The targeted protein searches establish that a homothallic (selfing) sexual cycle can occur in P. membranacea, but also shows evidence of a parasexual cycle. Two galectin-like genes, lec–1 and lec–2 were characterized and found to be differentially expressed. Lec–1 expression is enhanced by the presence of photobionts whereas lec–2 is highly polymorphic, suggesting strong positive selection, but apparently not driven by variation in photobiont partners. A high level of cytosine methylation (~13.4%,) was found in the genome with an average 2.7% and 8.2% present in exons and introns, respectively. Although all basic genes related to genome defense in ascomycetes were present, a key gene needed for repeat induced point mutation, rid, was absent. As the first comprehensive tissue-specific transcriptome and methylome analysis of a cyanolichen, this study lays a foundation for future functional genomics research on these widespread symbiotic organisms. Additionally, a lichen collected during field sampling was characterized as a new cyanolichen species and named as Peltigera islandica.

About the doctoral candidate:

Sheeba was born in Tamilnadu, India to G. Manoharan, an ex-serviceman of the Indian army, and M.L. Samathanam, a homemaker. She has a younger brother, Marshall, an IT consultant. 

Sheeba completed her high school from St. Joseph's Cluny Hr. Sec. school. She graduated with distinction from the Masters (M.Sc and M.Phil) program at Bharathidasan University, India. Before heading to UI for her Ph. D, she spent a couple of years working as a lecturer in Bangalore. She joined Prof. Dr. Olafur S. Andresson's group in 2008 and received a research scholarship from the University of Iceland in 2010 to work on Peltigera membranacea transcriptomics and methylomics. 

Sheeba is married to Dr. Basil Britto Xavier, a post-doctoral researcher, at the University of Antwerp and they have a daughter Benita Samara Basil.

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