About half of the genetic variation linked to phenotypic traits is thought to be caused by genetic variation in the non-coding genome, which remains poorly annotated for most species\u2019 genomes. Historically, transcription factor binding sites (TFBS), a key part of the regulatory non-coding genome, had to be arduously identified one transcription factor at a time, or genome-wide through the identification of open chromatin at the cost of interpretability. The novel MNase-defined cistrome-Occupancy Analysis (MOA-seq) provides a scalable approach without compromising on resolution. However, MOA-seq currently relies on the availability of assembled genome sequences, which often remain unavailable. Additionally, sequence quality is paramount for haplotype-specific analysis of TFBS performed in F1-hybrids to avoid trans-effects. This poses a problem both for large and complex genomes, but also for projects with a larger number of genotypes where long-read sequencing often remains unfeasible. We demonstrate the power of MOA-seq for haplotype-specific pan-cistrome analysis in maize, as well as develop novel strategies in barley based on published reference genomes and short-read sequencing. We evaluate these strategies by comparing commonly used SNP-replaced genomes with composite genomes generated based on a practical haplotype graph and genomes generated from long-read sequencing while showcasing the benefits and limitations of each method.<\/p>\n","protected":false},"excerpt":{"rendered":"
Annotating the cis-regulatory space of crop pan-genomes<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"_acf_changed":false},"categorie-seminaire":[],"class_list":["post-13822","seminaire","type-seminaire","status-publish","hentry","wpautop"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/seminaire\/13822","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/seminaire"}],"about":[{"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/types\/seminaire"}],"version-history":[{"count":2,"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/seminaire\/13822\/revisions"}],"predecessor-version":[{"id":13830,"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/seminaire\/13822\/revisions\/13830"}],"wp:attachment":[{"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/media?parent=13822"}],"wp:term":[{"taxonomy":"categorie-seminaire","embeddable":true,"href":"https:\/\/www.umr-diade.fr\/en\/wp-json\/wp\/v2\/categorie-seminaire?post=13822"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}