Section: New Results

NGS applications

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Fabrice Legeai.

• Participation to an international competition of assembly: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance and in their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. In this context, we have participated to the Assemblathon-2 competitions, which purpose was to assess current state-of-the-art methods in genome assembly. Globally, the cumulative z-scores of different assembly criteria set our assembly strategy in the 4th position compared to other competitors (21 groups). [12]

• Assembly on Raspberri Pi: Current Assembly tools require computers with large memory configuration. In order to demonstrate the efficiency of our low memory footprint assembly tools, we assemble the genome of C. Elegans (100 Mbp) on the raspberry PI computer, a small system equipped with only 512 MB RAM and 32 GB flash drive. [42]

• SNP detection on the tick We took part of a population genetic study on the tick species Ixodes ricinus, the main vector species of human and animal vector-borne diseases in Europe. In this framework, we proposed the first identification of a set of SNPs isolated from the genome of I. ricinus, by applying, among others a new tool developed in the GenScale team: discoSnp. The main advantage of this tool is to be able to detect SNPs without the use of a reference genome, which is crucially lacking for the tick species. Among the detected SNPs, 384 were selected, according to their minimal and maximal coverage and context sequences for experimental validation. Among them, 368 (95.8%) were biologically validated, demonstrating the precision of discoSNP.[23]

• NGS analyses on insect models We achieved the transcriptome assembly and analyzed the differential expression of an important noctuid pest. [22] , [18] . Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm theoretical models suggesting that the evolution of sex-biased gene expression may restrict the product of a sexually antagonistic allele to the sex it benefits.[19]

• Genome sequencing and annotation: We participated in the sequencing and annotation of several bacterial species of the Mollicute group. These bacteria are important pathogens of ruminants. The sequencing and annotation of their genomes confirmed their pathogenic features and phylogenetic location in the tree of Mollicutes. This is the first step before comparative genome analyses to unravel the genetic basis of mycoplasma pathogenicity and host specificity. [15] , [16] , [21]