Supervisors: Chris Jiggins, Richard Durbin Industrial partner: Miha Pipan (Entomics)
A PhD studentship is available to start from October 2018 on the genome and domestication of Hermetia illucens, commonly known as the black soldier fly (BSF), funded by the UK National Productivity Investment Fundthrough the Biotechnology and Biological Sciences Research Council.
By feeding on organic waste biomass, such as food, agricultural and manure wastes, BSF larvae are capable of converting waste biomass into a sustainable and renewable source of sought-after nutrients – BSF larvae are rich in lipids and proteins, and BSF larvae-derived meals are effective feedstuffs for a range of commonly farmed livestock species ranging from poultry to farmed fish. This project will study the genome of the BSF and apply population genetic and machine learning methods for analysis of the signatures of domestication in industrial strains.
We have already obtained a preliminary assembly of the BSF genome using a single Chromium 10X library with a total length of 1.1Gb and scaffold N50 of 1.05Mb. The sequenced individual was from a trio family for which further siblings are available. We have also established a stock derived entirely from the original founder pair that can be used for future genetic analysis. The studentship will improve the genome assembly, using long-read sequence for a single additional sibling individual and for the parents. This will permit a trio-based assembly approach whereby offspring reads are separated into haplotypes before assembly using parental kmers, from which we anticipate obtaining multi-megabase scale assemblies for both parental haplotypes. The genome will be annotated using publicly available transcriptome data, using the BRAKER pipeline, which we have used recently for annotation of butterfly genomes. An extensive RNAseq data set has already been published in which larvae were exposed to a variety of diets, providing a resource for annotation of larva-expressed genes.
To study the process of domestication we will obtain Illumina WGS resequencing data for a population sample of the industrial strain of BSF, and for least one outgroup population/species. The student will map these data to the reference genome, call genotypes and use both composite likelihood and machine learning approaches in order to scan the genome for regions that have been subject to recent selection. Genome regions that have been under adaptive selection during the process of domestication will be potential targets for future genetic manipulation of the BSF for further optimisation of its efficiency. In addition, comparison to other dipteran genome sequences will identify longer time frame patterns of conservation and evolutionary divergence.
The scheme is advertised here on FindaPhD.com