Additional file 2: Table S1. Information on motif analysis of CTCF Xi-peaks in Patski cells. Table S2. Information on escape domains on the X chromosome. Table S3. Information on allelic sgRNAs for CRISP/Cas9 editing and derived deletions and inversions. Table S4. Xi and Xa expression levels of eight escape genes in WT, Del-Firre and Del-Firre+tg. Table S5. Information on primers used

Additional file 2: Table S1. Information on motif analysis of CTCF Xi-peaks in Patski cells. Table S2. Information on escape domains on the X chromosome. Table S3. Information on allelic sgRNAs for CRISP/Cas9 editing and derived deletions and inversions. Table S4. Xi and Xa expression levels of eight escape genes in WT, Del-Firre and Del-Firre+tg. Table S5. Information on primers used

Xpresso: Predicting gene expression levels from genomic sequences

More info at:
Publication: https://doi.org/10.1016/j.celrep.2020.107663
Website: https://xpresso.gs.washington.edu/
Github: https://github.com/vagarwal87/Xpresso

Xpresso: Predicting gene expression levels from genomic sequences

More info at:
Publication: https://doi.org/10.1016/j.celrep.2020.107663
Website: https://xpresso.gs.washington.edu/
Github: https://github.com/vagarwal87/Xpresso

The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.

Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.