Res Sq 2026 May 20; doi: 10.21203/rs.3.rs-9490613/v1.

Sea Cucumber Holothuria glaberrima High-Quality Genome: new and extended gene families in Holothuroidea.

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The sea cucumber Holothuria glaberrima is a premier model for regenerative research that has allowed the discovery of key cellular and molecular characteristics of the intestinal and neuronal regeneration. However, the lack of a high-quality reference genome has limited molecular studies of regenerative processes in this species. We generated a chromosome-level genome assembly using PacBio long-read sequencing and Omni-C chromatin conformation capture data. In addition, assembly improvements were performed through manual curation and scaffolding with artificial mate-pairs from the short read draft genome assembly. The final assembly comprises 1.23 Gb with N50 of 50.9 Mb and 94% of genomic content within 23 chromosomal scaffolds. We identified 34,720 protein-coding genes and evaluated its quality through the analysis of the highly conserved gene families of Hox and Sox genes. In depth genomic analyses showed notable gene family expansions such as 51 THAP domain transcription factors and 37 SRCR domain-containing genes, representing significant increases compared to vertebrates. Furthermore, transposable elements annotation showed that these constitute ~ 50% of H. glaberrima's genome, with DNA transposons predominating over retrotransposons. Analysis of Gypsy retrotransposons showed upregulation during distinct stages of intestinal regeneration, with expression correlating to nearby regeneration-associated genes. This chromosome-level assembly enables sophisticated molecular studies of regenerative processes and establishes a framework for comparative genomic analyses with deuterostomes and other model species, significantly enhancing our understanding of the genetic basis underlying exceptional regenerative capacity in echinoderms.

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