Di Franco, A. | bioRxiv Science

bioRxiv2025

Comprehensive detection of structural variations in long and short reads dataset of French cattle

Structural variants (SVs) correspond to different types of genomic variants larger than 50 bp. Many findings suggest the use of long rather than short reads to improve the accuracy of SV detection. Here, we present the results of an in-depth analysis for detection of SVs, mainly large insertions and deletions, in 14 French bovine breeds, based on whole-genome data comprising 176 long-read and 571 short-read samples, with 154 individuals having both long- and short-read data available. We first investigated possible biases on the performances of well-known SV detection tools, namely CUTESV, PBSV, and SNIFFLES, using long reads from different technologies, including PacBio HiFi, Oxford ONT, and PacBio CLR. We subsequently highlighted the abilities of tools for detecting SVs (DELLY, LUMPY, and MANTA) and for genotyping known SVs (GRAPHTYPER, SVTYPER, PARAGRAPH, and VG toolkit) using short-read data. We then show how the incremental composition of samples in the reference panel affected the SV genotyping for six validation individuals sequenced in short reads. We then searched for the optimal parameters and created the final SV reference panel consisting of 25,191 deletions and 30,118 insertions. Finally, we emphasized the landscape of the genotyped SVs segregating across 571 short-read individuals of 14 breeds.

genomics↗

bioRxiv2021

Lower statistical support with larger datasets: insights from the Ochrophyta radiation

It is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion and plastid trees, it decreases in the nuclear tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that proper signal extraction is difficult to attain, as demonstrated by conflicting results obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.

evolutionary biology↗