Probes of capture of flanking regions at the S locus and control regions in A. halleri

We restricted our study to the entire S locus, i.e. the SCR and SRK genes with the intergenic regions, the flanking regions of the S locus and the control regions. The region of the S locus designed from the entire SRK sequences (n = 21) or partial SRK sequences of the S domain of SRK (n = 102, mean = 56% of the S domain) of different Brassicaceae species (A. halleri, A .lyrata, A. thaliana, A. kamchatica, Capsella grandiflora, C. rubella, Brassica rapa, B. oleracea). The fasta sequences are available on the database. The regions flanking at the S locus represent the 100,000 kb on either side of the S locus on two BAC clones of A. halleri. The control regions represent 25 kb regions having the same density of genes and transposable elements (TEs) as the flanking regions (+/- 10%) drawn at random from the genome of A. halleri. The fasta sequences are available on the database (ARABIDOPSIS-.input-seq.fas).The design and the synthesis of the probes were carried out by Mybaits with K-mers of 120 bp (ARABIDOPSIS-bait-120-60.fas). In order to ensure the specificity of the probes defined, we excluded TE from a set of transposable elements annotated in A. halleri and A. lyrata (Legrand et al., 2019), excluding 100 bp on both sides. of each sequence identified as repeated. We constructed probes with a recovery rate of 1.15, finally for a total of 48,127 probes (lit file). We verified that all target sites in the regions of interest such as the S locus genes were covered by at least one probe. Collectively, our initial goal was to cover at least 4.1MB per region. After excluding sites of low complexity and sites for which probes could not be defined, our sequence capture device covers 3.8 Mb (1.48%) of the genome of A. halleri.ARABIDOPSIS-.input-seq.fas=> fasta files with all regions studied in A. halleri and other brassicacees, based on BAC clones and the reference of A. halleri genome ARABIDOPSIS-bait-120-60.fas=> fasta file with all probes designed by MyBaits ARABIDOPSIS-bait-120-60-stringent_0RM.bed=> bed files with conserved probes