BIN6002 Été 2017 : Projects d'analyse

(version 05 mai 2017)

A. "PLOIDY" (Yasmine, Ying)
Project: Nuclear genome ploidy of unicellular eukaryotes with unknown life cycle.
Two eukaryotes will be analyzed: a jakobid, presumably diploid, and Diplonema papillatum, from which we know that the genome is neither (homogenously) haploid (1n) nor diploid (2n).
Biological questions: Based on the distribution of SNPs, is the genome diploid, triploid, tetraploid, etc., and/or of mixed ploidy (aneuploid or containing segmental duplications/triplications)?
Provided data: Illumina sequence reads, unpublished genome assembly and gff annotation file, a set of single-copy genes.
Proposed methodology:. map genomic sequence reads onto contigs of genome assembly; call variants on regions of contigs containing (i) single-copy genes; (ii) intergenic regions w/o repeats; generate a variant-frequency distribution for each contig, and for portions of it; compare distributions, group them; determine which theoretical distribution (for 1n, 2n, etc.) fits best the empirical distribution; infer the most likely ploidy.
Recommended hardware: Linux workstation or server with at least 290 GB RAM.
Supervision: Gertraud Burger, Robin Palvadeau

B. "IMPORT" (Anh-Tien, Lionnel, Gorgui)
Project: In silico identification of components involved in protein import into mitochondria of primitive eukaryotes (jakobids, malawimonads) and their derived relatives (diplonemids).
Biological question:What is the machinery's composition in the most primitve eukaryotes known, and how did it change during evolution? Is there a particular evolutionary trends e.g. toward streamlining or complexification?
Provided data:A list of TIM and TOM proteins (Acc. numbers) from model species; unpublished genome assemblies and gff annotation files, functional annotation.
Proposed methodology: collect and validate import proteins from model organisms; Identify additional homologs via BLAST, psi-BLAST and HMM-based HMMer seach in GenBank and in unpublished sequences from primitive and derived eukaryotes (Malawimonads, diplonemids); compare machinery composition with model organisms (yeast, plants, human, trypanosomes).
Recommended hardware: Linux workstation with >=32 GB RAM.
Supervision: B. Franz Lang, Matt Sarrasin.

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