Fig. 1: Genome assembly and annotation of holocentric L. sylvatica.

a Statistics of the L. sylvatica genome assembly and the final scaffolding. b BUSCO assessment for completeness of genic space with the viridiplantae_odb10 dataset, using the entire genome assembly. c Intra and inter-chromosome contact matrices of L. sylvatica. Color intensity represents contact frequency. Dark lines mark chromosomal boundaries. Boxes along the diagonal represent interactions within the same chromosome (cis), as expected for holocentric chromosomes. d Immunostaining of L. sylvatica holocentromeres using anti-CENH3 antibody (green). e L. sylvatica Chromosome 1 detailed view showing the dispersed density distribution of main genomic features: genes, CENH3, satellite DNA, LTR Ty1-copia, LTR Ty3-gypsy, H3K4me3 and H3K9me2 histone marks, and DNA methylation (CpG, CHG and CHH); as typical for holocentric chromosomes. Bin sizes of 100 kb. The distribution of features on all chromosomes is reported in Supplementary Fig. 2. f Plots of chromosome size, number of discrete CENH3 domains (units), their size (<700 kb shown), and density (units/Mb). The CENH3 unit size boxplot follows the definition in seaborn data visualization package where central lines represent median value, boxes represent 1st and 3rd quartiles, and whiskers represent the data range without outliers, defined as observations further than 1.5 of interquartile range from the respective (1st or 3rd) quartile. The number of observations (units) on each chromosome corresponds to the CENH3 unit count panel. Source data are provided as a Source Data file.