Oferta de doctorado estudiando moscas que transforman residuos orgánicos en alimento para animales

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 ĄV 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.

URGENT DEADLINE 30 June 2018
Contacts: c.jiggins@zoo.cam.ac.uk, rd109@gen.cam.ac.uk
The scheme is advertised here on FindaPhD.com
<https://www.findaphd.com/search/PhDDetails.aspx?CAID=3968&LID=290>

Professor of Evolutionary Biology (2014)
Department of Zoology
University of Cambridge
Tel: (+44)(0)1223 769021
Mob: (+44)(0) 7549-524-481
http://www.heliconius.org/
http://heliconius.zoo.cam.ac.uk/
@mel_rosina

Fellow of St John's College,
Cambridge, UK. CB2 1TP

The Ecology and Evolution of Heliconius Butterflies
Available through all good bookshops, or direct from Oxford University
Press