RP01: De novo assembly and functional annotation of the genome of Populus nigra

  • PhD Supervisor(s): Michele Morgante, Emanuele De Paoli, Federica Cattonaro
  • Host Institution: Institute of Applied Genomics (IGA) - Technology Services, Udine, Italy
  • Duration: 36 months.
  • Fixed start date: 1 April 2018
  • Planned secondment(s): ecSeq GmbH (DE), Philipps Universitaet Marburg (DE)

The aim of this project is to produce a high quality, annotated reference sequence of the Populus nigra (black poplar) genome in order to support structural and functional studies as well as enable high-resolution epigenetic analyses within the EpiDiverse consortium. Genome assembly will be informed by the available draft genome of a sister species, Populus trichocarpa and aimed at producing haplotype-specific assemblies for each of the two homologs present in the highly heterozygous individual chosen for sequencing. DNA/RNA library preparation and sequencing will be performed under the supervision of highly specialized staff in the laboratories of the hosting sequencing facility using long pseudo-read Next Generation Sequencing technologies. The application of state-of-the-art in silico analyses and experimentation of new computational methods, some of which developed in house, will yield an initial whole-genome draft that will be further assembled into large scaffolds using in situ Hi-C technologies. The phased assemblies of the two parental haplotypes will allow analysis of the intra-individual structural variation and will be employed to enable allele-specific analyses of gene expression and epigenetic determinants. The genome sequence will be further refined and completed with the addition of gene prediction and repeat element annotation. A specific focus will be placed on the analysis of the transposable element composition and the study of their evolution and insertional preferences using also existing sequencing data from additional Populus nigra accessions. The project will interact with other international research teams involved into the exploitation of poplar genomic information to explore ecologically relevant phenomena.

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