The purpose of this Framework Agreement is to produce genetic resources and datasets for Timema species. It includes whole genome resequencing (WGRS), production of several reference genomes, sequencing of epigenetic mechanisms, and genotyping by sequencing (ddRAD) of timema stick insects. This framework agreement is implemented within the framework of the ERC EE-Dynamics project "Dynamics of eco-evolutionary systems" (PI P. Nosil).

This service aims to impute the whole genome sequences of individuals of the genus Timema using a deep resequencing (10x) of the whole genome of individuals, in order to predict the sequence of the whole genome of other individuals with 0.5x coverage sequencing. The incumbent will be responsible for the preparation and sequencing of libraries. The DNA extractions will be sent by carrier in different batches of a hundred samples at a time.

The purpose of this batch is the sequencing of reference genomes with chromosomal scale assembly and haplotype resolution. We request several reference genomes for different morphs (with different dorsal motifs) in different species of the genus Timema.

The aim of the service is to perform epigenetic testing in T. cristinae from different host plant populations – which define ecotypes. We plan to obtain data for specimens of different host plants on:

1) DNA methylation status using the WGBS technique;

2) The high-resolution chromatin accessibility map using the ATAC-seq technique;

3) The three-dimensional organization of chromatin and a genomic map of interactions between loci using the Hi-C technique;

4) Map of histone modifications using ChIP-seq;

5) Expression models using the RNA-seq technique;

6) Evaluate the genetic structure underlying these epigenetic structures using WGS. We will supply the insect tissues and the service provider will perform the various treatments (i.e., bisulfite, ATAC, chromatin conformation capture) followed by high-resolution sequencing.

The purpose of this contract is to genotype by sequencing individuals of the species Timema cristinae. We will provide the holder with ready bookstores. The service provider will perform the sequencing of these libraries.