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Chromosome-level genome assembly of Hydractinia symbiolongicarpus
Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regula...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411563/ https://www.ncbi.nlm.nih.gov/pubmed/37294738 http://dx.doi.org/10.1093/g3journal/jkad107 |
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author | Kon-Nanjo, Koto Kon, Tetsuo Horkan, Helen R , Febrimarsa Steele, Robert E Cartwright, Paulyn Frank, Uri Simakov, Oleg |
author_facet | Kon-Nanjo, Koto Kon, Tetsuo Horkan, Helen R , Febrimarsa Steele, Robert E Cartwright, Paulyn Frank, Uri Simakov, Oleg |
author_sort | Kon-Nanjo, Koto |
collection | PubMed |
description | Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism. |
format | Online Article Text |
id | pubmed-10411563 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-104115632023-08-10 Chromosome-level genome assembly of Hydractinia symbiolongicarpus Kon-Nanjo, Koto Kon, Tetsuo Horkan, Helen R , Febrimarsa Steele, Robert E Cartwright, Paulyn Frank, Uri Simakov, Oleg G3 (Bethesda) Genome Report Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism. Oxford University Press 2023-05-18 /pmc/articles/PMC10411563/ /pubmed/37294738 http://dx.doi.org/10.1093/g3journal/jkad107 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genome Report Kon-Nanjo, Koto Kon, Tetsuo Horkan, Helen R , Febrimarsa Steele, Robert E Cartwright, Paulyn Frank, Uri Simakov, Oleg Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title | Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title_full | Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title_fullStr | Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title_full_unstemmed | Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title_short | Chromosome-level genome assembly of Hydractinia symbiolongicarpus |
title_sort | chromosome-level genome assembly of hydractinia symbiolongicarpus |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411563/ https://www.ncbi.nlm.nih.gov/pubmed/37294738 http://dx.doi.org/10.1093/g3journal/jkad107 |
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