SNIC SUPR
WGS lion
Dnr:

SNIC 2019/3-179

Type:

SNIC Medium Compute

Principal Investigator:

Göran Spong

Affiliation:

Sveriges lantbruksuniversitet

Start Date:

2019-03-31

End Date:

2020-04-01

Primary Classification:

10615: Evolutionary Biology

Webpage:

Allocation

Abstract

Reason for increased resource need: Our completed Falcon and wtdbg2 assemblies need to be supplemented by a MARVEL assembly, requiring more computing hours. The Crater lion population in northern Tanzania is small and believed to be isolated from neighbouring populations making it at risk of extirpation. With this project, we will assess the level of inbreeding that exists by analysing runs of homozygosity, one of the more sophisticated methods recently developed. To do this, we will use long read data to create a high quality whole genome assembly, which is necessary to properly analyse runs of homozygosity. We will then use this high quality assembly to align 17 whole genomes from lions throughout the Crater population. With these 18 genomes, we will determine the level of inbreeding in each individual, which will provide an estimate of inbreeding levels throughout the population. By doing this, we will be able to better assess the endangered status of the Crater lion population, while at the same time, providing a resource (high quality genome assembly) that will be valuable for many types studies of lion populations. This work will also form the base for an extended project looking at these question across three lions populations with similar histories across Africa.