ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/087/SRR29095787/SRR29095787_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/086/SRR29095786/SRR29095786_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/085/SRR29095785/SRR29095785_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/084/SRR29095784/SRR29095784_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/085/SRR29095785/SRR29095785_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/087/SRR29095787/SRR29095787_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/086/SRR29095786/SRR29095786_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR290/084/SRR29095784/SRR29095784_2.fastq.gzprimary200OKGenomicsSevinç Ercan, Biology, New York Universityhttps://www.ebi.ac.uk/ena/browser/view/PRJNA1113945Mechanisms of X chromosome dosage compensation have been studied in model organisms with distinct sex chromosome ancestry. However, the diversity of mechanisms as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, where dosage compensation is accomplished by an X chromosome specific condensin that belongs to the family of structural maintenance of chromosomes (SMC) complexes. By combining a phylogenetic analyses of the C. elegans dosage compensation complex with a comparative analysis of its epigenetic signatures, such as X-specific topologically associating domains (TADs) and enrichment of H4K20me1, we show that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis following an SMC-4 duplication. Unexpectedly, we found an independent duplication of SMC-4 in Pristionchus pacificus along with X-specific TADs and H4K20me1 enrichment, which suggests that condensin-mediated dosage compensation evolved more than once in nematodes. Differential expression analysis between sexes in several nematode species indicates that dosage compensation itself precedes the evolution of X-specific condensins. In Rhabditina, X-specific condensins may have evolved in the presence of an existing mechanism linked to H4K20 methylation as Oscheius tipulae X chromosomes are enriched for H4K20me1 without SMC-4 duplication or TADs. In contrast, Steinernema hermaphroditum lacks H4K20me1 enrichment, SMC-4 duplication, and TADs. Together, our results indicate that dosage compensation mechanisms continue to evolve in species with shared X chromosome ancestry, and SMC complexes may have been co-opted at least twice in nematodes, suggesting that the process of evolving chromosome wide gene regulatory mechanisms are constrained. Overall design: To examine the 3D genome structure of autosomes and X chromosomes in the nematodes Pristionchus pacificus and Oscheius tipulae, we performed Hi-C sequencing on early stage hermaphrodite larvae.xref:PubMed:38826443ENAfalseParallel evolution of X chromosome-specific SMC complexes in two nematode lineages [Hi-C]Parallel evolution of X chromosome-specific SMC complexes in two nematode lineages [Hi-C]2025-08-072024-06-23PRJNA1113945GSE26796338826443