RADdesigner: a workflow to select the optimal sequencing methodology in genotyping experiments on woody plant species

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomicticRanunculus auricomuscomplex (Ranunculaceae)

“…2). However, de novo assembly of RADseq reads remains methodically challenging considering various genomic divergence levels within and among individuals/species (see e.g., Guillardín-Calvo & al., 2019; Pätzold & al., 2019; Rancilhac & al., 2019).…”

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

“…Obtaining candidate loci in reduced genome representation studies (ddRADseq), particularly if they are aimed to perform individual classification of hybrids, requires careful experimental design to ensure sufficient coverage of the genome of the focal species and rigorous filtering of variants in order to minimize the potential sources of error in marker identification ( O’Leary et al., 2018 ). In the present work, an experimental design derived from a pilot study ( Guillardín-Calvo et al., 2019 ), together with an ad hoc bioinformatic pipeline has enabled the identification of a significant number of genomic markers to analyze ongoing hybridization between Q. ilex and Q. suber .…”

“…For ddRADseq analysis of all samples, a pilot study was conducted using the protocol implemented on RADdesigner ( Guillardín-Calvo et al., 2019 ) to assess the optimal enzyme combination, type of library, and number of reads per sample for the aims of the study. Based on this pilot study, PstI/MspI were selected as restriction enzymes.…”

NGScloud2: optimized bioinformatic analysis using Amazon Web Services

“…The correct operability of the pipelines for de novo RNAseq, reference-based RNAseq, RADseq and funcional annotation was tested with data generated by our research group. Guillardín-Calvo et al, 2019). Read data are available at NCBI: SRX5228139 -SRX5228161 for Pcan, and SRX5019123-SRX5019138 for Suberintro.…”

“…ddRADseq) are used to find out polymorphism in specific genomic regions nearby restriction enzyme cut sites in populations of multiple individuals, and has revealed powerful in phylogenetics, population genetics, and association mapping studies, among others (Andrews et al, 2016). In NGScloud2, we have included ddRADseqTools (Mora-Márquez et al, 2017) and RADdesigner (Guillardín-Calvo et al, 2019) to assess the optimal experimental design of a RADseq experiment, i.e. to choose the enzyme combinations, simulate the effect of allele dropout and PCR duplicates on coverage, quantify genotyping errors, optimize polymorphism detection parameters or determine sequencing depth coverage.…”