Abstract
Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.
Highlights
Regeneration, the replacement of lost or damaged body parts, is one of the most fascinating biological processes
We show the utility of our draft nuclear genome by using it to ascertain the genomic structure of melanotransferrins, proteins that might play important roles in the regeneration process (Rojas-Cartagena et al, 2007; Hernández-Pasos et al, 2017)
We further evaluated our genome assembly by closely examining H. glaberrima genes that had been previously described in studies based on expressed sequence tags (EST), RNA sequencing, and/or Sanger-based cDNA sequencing
Summary
Regeneration, the replacement of lost or damaged body parts, is one of the most fascinating biological processes. We have reported gene expression profiles of various stages of regeneration, providing information on which genes play important roles in sea cucumber regenerative processes (Ortiz-Pineda et al, 2009; Mashanov et al, 2014). These RNA-Seq analyses have led to interesting findings, but the lack of a reference genome has limited the impact of these results. Both nuclear and mitochondrial genomic data will be useful for future studies in systematics, immunology, and evolution, among others
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