SNIC
SUPR
SNIC SUPR
De-novo spruce genome PacBio data assembly
Dnr:

SNIC 2018/3-317

Type:

SNAC Medium

Principal Investigator:

Nicolas Delhomme

Affiliation:

Umeå universitet

Start Date:

2018-06-18

End Date:

2019-07-01

Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Tertiary Classification:

40104: Forest Science

Allocation

Abstract

This project is the follow up on the original spruce genome project. We have generated data using the latest sequencing technologies and have set up a collaboration with the authors of the salamander genome project (https://www.nature.com/articles/nature25458), which has released the largest genome ever released using long read sequencing technologies to date. Our project aims at assembling 2 conifer genomes, these of the Norway spruce and of Scots pine, both of which are over 20 Gbp in size. Both these species are of essential economical and ecological importance to Sweden. The current assemblies for these species are extremely fragmented and contains several millions of scaffolds in stance of the expected 12 chromosomes. In other words, their use is severely limited; i.e. they can be used for expression profiling but little more. Using the latest sequencing technology and assembly methodologies will allow us to get genomes of much better quality, which will unleash a lot of genomics and genetics studies that were impossible to date. Releasing these genomes will have a strong impact on the plant science field at large, but not only, as these would be the first plant genomes, not to mention the largest, to be published that were solely assembled from long 3rd generation sequencing data. These genomes will be important resources for the Swedish scientific community from basic research (e.g. looking at genome evolution) to applied research (e.g. breeding studies). As we have already received the data and as the main developer of MARVEL (the assembler used in the salamander project), will be coming to Sweden next week, we would appreciate if this proposal could be assessed shortly. That would give us the opportunity to get a fantastic head-start into that project, but I of course understand that this is a very short notice! Do not hesitate to contact me, Björn Nystedt at ScilifeLab (bjorn.nystedt@scilifelab.se) or Nathaniel Street (nathaniel.street@umu.se) if you needed any more details about this project.