Pacific Biosciences of California Inc (PACB)

[Paulieme]

Vacancy Details: Potato genomics (Computational Biologist)
Improving potato genetics using the long read sequencing data
Expected/Ideal Start Date 01 Aug 2014
Months Duration 36
Main purpose of the job To develop genetic resources in potato through the use of genomic technologies: assemble the genome of a diploid self-compatible relative from a mix of short (Illumina) and long read (PacBio/Nanopore) technologies; use next generation sequencing to harness induced variance (TILLING) that affects key traits and naturally occurring variance that confers resistance to common potato diseases.
Department Genomics
Group Details Plant and Microbial Genomics (PMG) group is a multi-disciplinary team with a strong technical expertise base in genetics, genomics, molecular biology, plant biology, bioinformatics. We are applying many of the latest sequencing technology improvements, and our own innovations, to the areas of plant and microbial genomics, and the interaction between the two.
See http://www.tgac.ac.uk/plant-and-microbial-genomics/ for more details
Advert Text Potatoes are the fourth most valuable crop in the world, yet despite a fully sequenced genome the available genetic resources are surprisingly sparse. One major hindrance is that potatoes (S. tuberosum) are an autotetraploid outbreeder, which hinders examination of recessive alleles. For this reason we will establish a tuber forming close relative S. verrucosum (an inbreeding diploid) as a genetic model by sequencing its genome and demonstrate its efficacy by cloning forward genetic EMS induced mutants. In a further grant we will harness naturally occurring potato variation in dominant traits i.e. NB-LRR based disease resistance using an improved version of RenSeq (Juppe et al. 2013).
The post holder will work at the cutting edge of next generation sequencing in a multi-disciplinary team with expertise in genetics, genomics, molecular biology, plant biology, bioinformatics and algorithm development. The successful applicant will use and optimise tools for assembling a large plant gene sequences and an entire genome using ultra-long Pacific Bioscience (and as available Nanopore) reads, as well as using shorter Illumina reads to verify and correct the assembly.

Key relationships Internal: working closely with Plant Microbial Genomics and Platform and Pipeline staff developing the wet lab (molecular biology) techniques, reporting to the Plant Microbial Genomics group leader.
Interacting with: all TGAC staff, especially the sequencing production teams, and the Computational Biology and Pipeline bioinformatics groups.
External: key biology collaborators at James Hutton Institute, University of Dundee, The Sainsbury Laboratory and Simplot (a world leading Agri-Biotechnology company), platform providers e.g. PacBio, Oxford Nanopore Technologies, and Illumina as well as potato geneticists and breeders. The post holder will represent TGAC at key meetings nationally and worldwide.

Main Activities & Responsibilities Percentage
To establish optimal systems for handling and assembling 3rd generation long read e.g. PacBio and/or Nanopore data. 30
To work with key members of the Plant Microbial Genomics and Computational Biology groups to develop optimal experimental and computational approaches to assemble the inbred diploid potato species S. verrucosum. 20
Use hybrid sequence data (long and short reads) to separate large highly related gene families. 15
Use hybrid sequence data to identify naturally occurring variance in large gene families that confer desirable traits 15
Use next generation sequencing short reads to map EMS induced alleles e.g. from bulk segregant pools. 10
Prepare talks and publications on in-depth analysis of population genomics data sets generated at TGAC, or with collaborators. 10
http://jobs.tgac.ac.uk/Details.asp?vacancyID=7851