Biology subjects
Publications and source records attributed to Stenger, P.-L..
AGR, for Ancestral Genome Reconstruction, is an automatic publicly available and open-source pipeline to infer paleogenomes from modern species genome comparisons exploiting the concept of inter-species chromosomal synteny relationships hierarchical clustering that can be used to unveil how ancestral genomes, genes, sequences and functions have been shaped during million years of present-day plant evolution.
Chromatin Immunoprecipitation sequencing (ChIP-seq) is the method of choice to generate chromatin landscapes across genomes. The scarcity of literature on ChIPseq and absence of a canonical "gold standard" method in mollusks and especially the pacific oyster Magallana gigas, prompted us to compare four ChIP-seq methodologies (Native-ChIP, Crosslink-ChIP, ChIPmentation and Cut & Tag) to find the most suitable method for this species. Our results show that Cut & Tag performs best and ChIPmentation worst. We hypothesize that the reason for this lies in a particularly fragile chromatin structure around genes in the oyster.