2.3. Characterization of Satellitome and BLAST Search of VchSatDNAs

The satellitome of males and females of V. chilensis were independently characterized by the Tandem Repeat Analyzer (TAREAN) tool [40]. We performed an initial assessment of the read quality (Q > 20 for all nucleotides) by using the trimmomatic software version 3 [41]. Then, as an input for the TAREAN clustering [40], we selected a random subset of 2 × 500,000 reads. The satDNAs recovered were filtered by the DeconSeq software version 0.4.3 [42] from the original subset of 2 × 500,000 reads, which were further loaded in TAREAN until no new satDNAs were identified. We removed other types of repetitive DNAs (e.g., multigene families) from the V. chilensis satellitome and assembled them into variants (>95% similar), families (80–95% similar), and superfamilies (50–80% similar) by using RM_Homology (https://github.com/fjruizruano/satminer/blob/master/rm_homology.py (accessed on 19 December 2023)) and Geneious software version 8.1 [11]. Finally, to estimate the abundance (mapped reads divided by the number of total nucleotides) and divergence (Kimura-2-parameter) of VchSatDNAs, we used a combination of a custom python script (https://github.com/fjruizruano/ngs-protocols/blob/master/repeat_masker_run_big.py, accessed on 20 December 2023) and the RepeatMasker softwareversion 4.1.6 [43]. Specifically, we selected 2 × 5,000,000 reads of each genomic library (male and female) and aligned them against their satDNA catalogs. Each VchSatDNA was named and numbered following the suggestions from Ruiz-Ruano et al. [11] and further represented in the form of repeat landscapes. To check for putative female-biased satDNAs, we calculated the female/male (F/M) abundance ratio of each VchSatDNA. Finally, we conducted a BLAST search [44] of all VchSatDNAs against the GenBank/NCBI (nucleotide collection) and Repbase databases (CENSOR) to verify the sharing of conserved DNA motifs with other closely related species and repetitive DNA sequences.