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The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus)
Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953449/ https://www.ncbi.nlm.nih.gov/pubmed/29763462 http://dx.doi.org/10.1371/journal.pone.0197371 |
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author | Yuan, Zihao Zhou, Tao Bao, Lisui Liu, Shikai Shi, Huitong Yang, Yujia Gao, Dongya Dunham, Rex Waldbieser, Geoff Liu, Zhanjiang |
author_facet | Yuan, Zihao Zhou, Tao Bao, Lisui Liu, Shikai Shi, Huitong Yang, Yujia Gao, Dongya Dunham, Rex Waldbieser, Geoff Liu, Zhanjiang |
author_sort | Yuan, Zihao |
collection | PubMed |
description | Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions. |
format | Online Article Text |
id | pubmed-5953449 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-59534492018-05-25 The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) Yuan, Zihao Zhou, Tao Bao, Lisui Liu, Shikai Shi, Huitong Yang, Yujia Gao, Dongya Dunham, Rex Waldbieser, Geoff Liu, Zhanjiang PLoS One Research Article Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions. Public Library of Science 2018-05-15 /pmc/articles/PMC5953449/ /pubmed/29763462 http://dx.doi.org/10.1371/journal.pone.0197371 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Yuan, Zihao Zhou, Tao Bao, Lisui Liu, Shikai Shi, Huitong Yang, Yujia Gao, Dongya Dunham, Rex Waldbieser, Geoff Liu, Zhanjiang The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title | The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title_full | The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title_fullStr | The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title_full_unstemmed | The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title_short | The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus) |
title_sort | annotation of repetitive elements in the genome of channel catfish (ictalurus punctatus) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953449/ https://www.ncbi.nlm.nih.gov/pubmed/29763462 http://dx.doi.org/10.1371/journal.pone.0197371 |
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