Profile
Project Title: Transforming meiofaunal molecular systematics and community ecology through nanopore-based transcriptomics.
Summary: Meiofauna are diverse communities of microscopic invertebrates, such as those living between grains of sand. Roughly 2/3 of all animal phyla are represented by at least one meiofaunal species. Many species remain undescribed, and many described species remain urgently in need of taxonomic revision. Meiofauna act both as key trophic links between microbes and macrofaunal species, and as players in broader biogeochemical processes. Short generational turnovers, in combination with the abundance, phyletic diversity, and intricate inter-species interactions, allow meiofauna to act as uniquely effective monitors for ecological changes. In particular, to monitor habitats threatened by anthropogenic change such as seagrass meadows, and temperate rainforests.
During this project, we will use explore applications of low-depth, long-read cDNA sequencing, or “transcriptome skimming”, to meiofaunal biodiversity, systematics, and molecular ecology. This technique provides ~50,000 reads per sample at low cost (ca. £10) and relatively little labour and can also capture transcripts expressed by any symbionts or gut contents. We have found such data is sufficient to assemble hundreds of highly expressed transcripts per individual, including many phylogenetically useful housekeeping genes. This project focuses on the development of bioinformatic tools and software to assemble and analysehigh-quality transcriptomes. Using these data, we aim to iteratively build large phylogenetic trees to position many species at a time, at a community level. Automated techniques such as this will hopefully be transformative for the study of meiofaunal biodiversity and systematics in a time of rapid environmental change.
Supervisor:
- Prof Yannick Wurm (SBBS)
- Dr Christopher Laumer (NHM)