Characterising gene function, biosynthetic pathways, and variation in agri/aquacultural traits

Functional annotation across eukaryotic species

Functional annotation is the comprehensive process of analysing genomic sequences to accurately identify and map genes and other functional elements to their correct locations within the genome, and to assign biological functions to these elements, such as genes, regulatory regions, and non-coding RNAs.

This involves the use of computational tools and biological databases to predict gene structures, identify protein-coding regions, assign functional roles, and integrate diverse biological data - ultimately providing a deeper understanding of the molecular mechanisms underlying biological processes and genetic traits.

A significant proportion of genes remain unannotated. This is a major problem in non-model species but, even in well-studied organisms, around 20 per cent of genes have no known function. This remains a significant barrier to understanding living systems and there is a pressing need for methodologies that can be applied at scale to close this knowledge gap.

Large-scale genome sampling, in projects such as the Darwin Tree of Life, offers new opportunities to apply phylogenetic profiling to this problem.

We will use phylogenetic profiling combined with transcriptional perturbation data to generete a database of co-expressed and co-evolving gene networks that can be used to infer gene function.

Genetic basis of plant bioactives

Plants produce a vast array of biologically active metabolites that help them adapt and survive.

This chemical richness provides a wealth of bioactivity with potential applications in medicine, agriculture and industry. However, while the bioactivities of plant extracts are frequently reported, the specific molecule, or molecules, responsible are often unknown.

Understanding the genetic basis of natural products, therefore, provides new opportunities for the scalable production of useful compounds.

With the Royal Botanic Gardens, Kew, this work will provide insights into the origins of novel chemodiversity in plants, as well as routes to access and manufacture molecules of interest to industry, health, and agriculture.

Genetic diversity in agri/aquacultural traits

During controlled breeding programs or natural hybridisation events, materials from gene pools from related species can introgress, generating hybrid admixed genotypes that potentially have increased genetic diversity.

This genetic diversity is likely to be an important source of genetic and phenotypic variation for key adaptive traits in the future. However, these events and their functional impacts are difficult to identify.

The full extent of chromosomal rearrangements and large structural variation is only beginning to become clear as we move from single to multiple assembled reference genomes, and from short-read to long-read sequencing technology.

New tools and methods developed in the Decoding Biodiversity research programme will aim to understand the underlying genomic processes and extent of this variation.