• Research group

Swarbreck Group

Understanding the complexity of eukaryotic transcriptomes and gene regulation.

Group leader
David Swarbreck

Group activities.

Our group explores the complexity of gene expression, mainly in plants (such as Ash, Rubber, Willow, Barley and Wheat), but also in other eukaryotic organisms.

The production of a high-quality reference genome annotation for a species is of critical importance for downstream analyses, but many plant genomes present significant challenges for genome assembly, due to large genome sizes, high repeat content, heterozygosity and polyploidy. As such, most of the sequenced plant genomes are of a draft standard and highly fragmented, compromising analyses of their sequence conservation, variation, and functionality.

Our research involves the development of sequencing, assembly, and annotation strategies to characterise transcriptome complexity including coding and non-coding transcripts, alternative splice variants and small peptides. 

Precise patterns of spatial and temporal gene expression are crucial for growth and development of multicellular eukaryotes and their response to the environment. Protein synthesis therefore requires tight regulation with multiple layers of regulation including transcription initiation, post transcriptional modification, mRNA degradation and translation. The group apply RNA sequencing coupled with complementary data (Chip-seq, BS-seq, ribosomal profiling) to explore the complexity of eukaryotic transcriptional landscapes.

Tools.

RAMPART
A workflow management system for de novo genome assembly.

Mikado
A method to leverage multiple transcriptome assembly methods for improved gene structure annotation.

PAREnet
For degradome assisted discovery and visualization of small RNA/target interaction networks.

Portcullis
A tool for junction analysis and spliced read alignment filtering.