Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration

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 g...

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Main Authors: Joshua G. Medina-Feliciano, Stacy Pirro, Jose E. García-Arrarás, Vladimir Mashanov, Joseph F. Ryan
Format: Article
Language:English
Published: Frontiers Media S.A. 2021-04-01
Series:Frontiers in Marine Science
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fmars.2021.603410/full
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spelling doaj-7506e683f67d4da5912c469485b56b0d2021-04-15T16:04:13ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452021-04-01810.3389/fmars.2021.603410603410Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of RegenerationJoshua G. Medina-Feliciano0Stacy Pirro1Jose E. García-Arrarás2Vladimir Mashanov3Joseph F. Ryan4Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, PR, United StatesIridian Genomes, Inc., Bethesda, MD, United StatesBiology Department, University of Puerto Rico, Río Piedras Campus, San Juan, PR, United StatesWake Forest Institute for Regenerative Medicine, Winston Salem, NC, United StatesWhitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United StatesRegeneration 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.https://www.frontiersin.org/articles/10.3389/fmars.2021.603410/fullholothuroidechinodermregenerationmelanotransferrinmitochondrial genome
collection DOAJ
language English
format Article
sources DOAJ
author Joshua G. Medina-Feliciano
Stacy Pirro
Jose E. García-Arrarás
Vladimir Mashanov
Joseph F. Ryan
spellingShingle Joshua G. Medina-Feliciano
Stacy Pirro
Jose E. García-Arrarás
Vladimir Mashanov
Joseph F. Ryan
Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
Frontiers in Marine Science
holothuroid
echinoderm
regeneration
melanotransferrin
mitochondrial genome
author_facet Joshua G. Medina-Feliciano
Stacy Pirro
Jose E. García-Arrarás
Vladimir Mashanov
Joseph F. Ryan
author_sort Joshua G. Medina-Feliciano
title Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
title_short Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
title_full Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
title_fullStr Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
title_full_unstemmed Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
title_sort draft genome of the sea cucumber holothuria glaberrima, a model for the study of regeneration
publisher Frontiers Media S.A.
series Frontiers in Marine Science
issn 2296-7745
publishDate 2021-04-01
description 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.
topic holothuroid
echinoderm
regeneration
melanotransferrin
mitochondrial genome
url https://www.frontiersin.org/articles/10.3389/fmars.2021.603410/full
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