Castro-Marquez, S. O. | bioRxiv Science

bioRxiv2026

A draft de novo assembly of Diadema antillarum, a keystone herbivore of the Caribbean reefs

We generated the first reference-level nuclear genome assembly of the keystone Caribbean long-spined black sea urchin species, Diadema antillarum (Philippi, 1845). Using whole-genome sequencing data from PacBio HiFi, Oxford Nanopore, and Illumina platforms, we employed multiple assembly strategies to generate a high-quality, near-complete genome. The final assembly spans 1.73 Gbp, consists of 2,964 scaffolds, and has an N50 of 1.56 Mbp. BUSCO analysis (metazoa_odb10) indicates 98.4% completeness. The genome displays a heterozygosity rate of 2.52% and contains 42.85% repetitive elements, of which 29.96% are unclassified. Coverage analysis reveals that while most of the genome was assembled at 11x depth, certain regions exhibit up to 530x coverage. Notably, regions exceeding 33x coverage account for 30.53% of the repetitive content, suggesting localized expansion of repeats. Duplication analysis of the assembled contigs shows that approximately 66% of contigs have duplicated, which supports segmental genome duplication in the past, and is further evidenced by the moderate level of heterozygosity of the assembly. While these characteristics contribute to the complexity of the genome, they do not diminish the quality of our assembly. Despite this complexity, our assembly maintains high completeness and contiguity. Our assembly provides a valuable resource for future genetic studies and serves as a critical framework for conservation, monitoring, and restoration of D. antillarum populations across the Caribbean.

genetics↗

bioRxiv2020

Genome Diversity in Ukraine

The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for the public data release. DNBSEQ-G50 sequences, and genotypes by an Illumina GWAS chip were cross-validated on multiple samples, and additionally referenced to one sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. The genome data has been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, CNVs, SNPs and microsatellites. This study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for historic and medical research in a large understudied population. While most of the common variation is shared with other European populations, this survey of population variation contributes a number of novel SNPs and structural variants that have not been reported in the gnomAD/1KG databases representing global distribution of genomic variation. These endemic variants will become a valuable resource for designing future population and clinical studies, help address questions about ancestry and admixture, and will fill a missing place in the puzzle characterizing human population diversity in Eastern Europe. Our results indicate that genetic diversity of the Ukrainian population is uniquely shaped by the evolutionary and demographic forces, and cannot be ignored in the future genetic and biomedical studies. This data will contribute a wealth of new information bringing forth different risk and/or protective alleles. The newly discovered low frequency and local variants can be added to the current genotyping arrays for genome wide association studies, clinical trials, and in genome assessment of proliferating cancer cells.

genomics↗