The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and genetic divergence of the haplotypes

Recent advances in sequencing technologies have improved contiguity of de novo genome assemblies. Nevertheless, the genomes of all non -haploid eukaryotic organisms remain unfinished, limiting understanding of genetic and structural variation in complex organisms. Herein, we report the methodology and analysis of a 100 % complete, telomere-to-telomere genome assembly of the eukaryote, Scenedesmus obliquus UTEX 3031 (DOE0152Z) with fully assembled and resolved haplotypes for 16 of 17 chromosomes. Inter-haplotype heterozygosity was significant on most chromosomes yet one chromosome pair (Chromosome 15) was found to contain nearly no heterozygosity, prohibiting full phasing of this chromosome. Analysis of the 5mC methylation patterns revealed divergence in active gene content across haplotypes. Assembly of fully resolved chromosome pairs enabled complete resolution of genomic rearrangements revealing significant heterozygosity of the haplotypes, the genomic basis of trait gain/loss, and evolutionary divergence across chromosome pairs. Further, when combined with 5mC methylation patterns, the assembly provides critical annotation information for genetic engineering approaches to achieve full knock-outs in allelic pairs.