Comparative Genomics of Non-Model Invertebrates

ESR Project 11: Assembly and annotation of heterozygous insect genomes

Supervisor: Denis Tagu (INRA Rennes), Co-supervisor Dominique Lavenier (INRIA, Rennes)

StudentAnne Guichard

Objectives: Although there are countless initiatives such as i5K for sequencing insects, these efforts are hampered by their often complex, very large, and highly heterozygous genomes. New hybrid assembly strategies using both short (Illumina) and long reads (Oxford Nanopore/PacBio), as well as approaches based on chromosome conformation capture (3C) may be used to alleviate these problems. This project will aim to test new approaches for increasing the quality of the assembly of large and complex heterozygous genomes with the aim to infer different traits (host recognition, reproduction) involved in the adaptation of target insect species to their environment.

O1: Analyse raw sequencing data from a set of insects of agricultural interest, Acyrthosiphon pisum, Dysaphis plantagineae, Spodoptera littoralis and frugiperda, Melinaea marseus, Ixodes ricines.

O2: Test and optimize available assembling strategies and programs on these genomes and to assess the quality of the resulting assemblies.

O3: Test and optimize automatic annotation procedures using expression data (RNA-Seq), k-mer-based approaches (in collaboration with ESR14), dedicated databases (Uniprot), and specific databases (of closely related species).

O4: Provide a web interface for browsing, blasting, annotating genomes on the IGNITE GALAXY server hosted at P4-BADW-LRZ.
Secondments: Dominique Lavenier (INRIA, Rennes), Jean-François Flot (Brussels), Michael Schrödl (Munich).

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