Subject 3 (C.

POUX) – 45mn – 7 points

Q1 3 points. Lesur et al (2018) designed a targeted capture-based, next-generation

sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur)
reference genome, for the sequencing of 3 Mb of genic and intergenic regions.

Figure 1: Correlation between sequencing depth and

genomic capture efficiency parameters. (A) Mean number of reads aligned with target sequences, (B)
mean number of SNPs per sample, (C) number of captured target sequences, and (D) target
sequence length.
Table 1 Statistics of the replicated samples.

a. Please explain what is the sequencing depth

b. The figure 1 represent the correlation between sequencing depth and genomic
capture efficiency parameters. Can you comment on the results?

c. The genomic capture assay was repeated twice for three oak genotypes of the Petite
Charnie population (Table 1). What can you say about the number of captured
targets and the length of the capture sequence for each genotype? Why do you
think the researchers wanted to repeat the analysis twice for several genotypes?
Can they be confident about their results?

Q2 2 points. What are the main differences between bacterial and eukaryotic genomes
(structure and content)?

Q3 2.5 points. Harvey et al. (2016) have examined the impact of a range of similarity
thresholds on assembly of empirical short read datasets from populations of four
different non-model bird lineages (species or species pairs) with different levels of
genetic divergence. Selecting the most appropriate similarity threshold is challenging,
primarily because the amount of genetic (allelic) variation can vary greatly among
orthologous loci within a species. Because the amount of genetic variation also varies
among species and genomic regions, a particular similarity threshold may impact each
dataset differently, potentially influencing inferences in comparative studies.

- Dashed lines: putative over-split loci

- Solid lines: putative under-split loci………

Figure 2 The impact of similarity thresholds on empirical datasets from four bird lineages.
Figure 3 The impact of similarity threshold on mean pairwise distance between the individuals
for four bird lineages (pairwise distance: measure of distance between each pair of sequences,
gives a level of dissimilarity between sequences).

a. Please explain what is the similarity threshold

b. Please explain the results of figure 2
c. Please explain how the similarity threshold can influence the average genetic distance at a
given locus.