Comparative Genomics of Non-Model Invertebrates

ESR Project 4: Comparative single-cell transcriptomics in sponges and placozoans

Supervisor: Detlev Arendt (EMBL Heidelberg), Co-supervisor Gert Wörheide (LMU Munich)

Student: Fabian Ruperti

Objectives: The nature of the last common ancestor of the Metazoa is largely unsolved, due to uncertainties in the branching pattern of non-bilaterian clades and, consequently, in the significance of the apparent morphological simplicity. For instance, our understanding and interpretation of the simple body plan of sponges and placozoa largely depends on their actual position in the animal tree of life. If they branched off early, they may be primarily simple; should they be closer related to cnidarians than for instance ctenophores, they probably underwent secondary simplification. One way to decide between these hypotheses is to examine their cell-type complexity. The PhD student of project 4 will closely interact with students of projects 1 & 2, who will generate novel genomes for species of three sponge classes, as well as on one placozoan species cultured at LMU Munich, by selecting those as experimental species.

O1: Establish cell dissociation protocols and single-cell sequencing protocols. For sponges, different life-cycle stages will be covered.

O2: Sequence cells with at least 1x coverage with regard to the total number of cells, to capture all cell types.

O3: Analyse single-cell transcriptomes with an established bioinformatics normalization pipeline for intra- and interspecific comparison.
Secondments: Grace McCormack (Galway), Gert Wörheide (Munich), Lyubomir Penev (Pensoft Publishers, Sofia).
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