Extended Data Fig. 3: The skate genome is organized in A/B compartments.

a. 500 kb resolution Pearson matrices of a representative chromosome (Leri_11C) and their associated eigenvectors showing marked compartmentalization in A/B compartments in both replicates. b. Eigenvector correlation among the two replicates. c. Merged Pearson matrix presented together with its eigenvector, the normalized signal for ATAC-seq in anterior pectoral fin, the number of gene models and the percentage of GC content. As shown in d, the A compartment in skates correlates with chromatin accessibility and the number of gene models, but no clear correlation was observed with the GC content. e. Saddle plot demonstrating the aggregated enrichment of homotypic A-A and B-B interactions. f. Gene expression in either the A or the B compartment as measured with bulk RNA-seq performed in the anterior and posterior portions of the skate pectoral fin at Stg 30. Top: anterior, bottom: posterior, n = 4046 bins of 500kb (A compartment n = 2125, B compartment n = 1921). Boxes correspond to the median and the first and third quartiles (Q1 and Q3). Whiskers extend to the last point within 1.5 times the interquartile range below and above Q1 and Q3, respectively.