Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome

Abstract

The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

“…The possibility of reconstructing private sequences from high-throughput resequencing data is still a challenge today 28 . For this reason, the last step in the SUPER-CAP workflow allows to specifically insert the detected variants into the sequence of each sample.…”

“…SUPER-CAP includes an updated version of SUPER-W (release 4) 28 . SUPER-CAP is a user-friendly web tool which only needs two input files to work: the captured region file in BED format and the filtered NGS reads in FASTQ format.…”

“…This lack of easily accessible software pushed us to propose a web-based tool, named SUPER-CAP (http://supercap.sequentiabiotech.com/), to boost quick, proficient and affordable analysis of sequence capture data. This tool, benefitting from SUPER-W pipeline 28 and combining different software and customizable procedures, assists the user in sequence capture experiments from the identification of single-nucleotide variants (SNVs) and small insertions and deletions (INDELs) to the reconstruction of genotype-specific (hereafter referred to as ‘private’) sequences/gene features for each target region of each sample.…”

Careful with That Axe, Gene, Genome Perturbation after a PEG-Mediated Protoplast Transformation in Fusarium verticillioides

“…This analysis highlighted genetic variations of Fv10027_t1 with the other strains (Fv10027_t0, ΔFv_ lds1 T, ΔFv_ lds1 D and FvHph + ). The open source pipeline SUPER-W [24] has been used for this purpose. Overall, 285,588 raw variants have been found: namely, 273,744 are SNPs, and 11,844 are DIPs.…”

Pentatricopeptide repeat 336 as the candidate gene for paternal sorting of mitochondria (Psm) in cucumber

“…Sequences were aligned to scaffolds 02047 and 03356 of the Gy14 reference sequence (Yang et al 2012) which span the region where Psm mapped (Calderón et al 2012). The pipeline Simply Unified Pair-End Re-sequencing Workflow (SUPERW) was used to reveal SNPs between sequences of P3A, Csh, and the Gy14 reference (Sanseverino et al 2015). Reads were aligned with Burrows-Wheeler Aligner (Li and Durbin 2009), followed by SNP calling with Samtools MpileUp and PileUp (Li et al 2009).…”