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Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development
BACKGROUND: Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029161/ https://www.ncbi.nlm.nih.gov/pubmed/24618421 http://dx.doi.org/10.1186/1471-2164-15-186 |
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author | Sun, Cheng Wyngaard, Grace Walton, D Brian Wichman, Holly A Mueller, Rachel Lockridge |
author_facet | Sun, Cheng Wyngaard, Grace Walton, D Brian Wichman, Holly A Mueller, Rachel Lockridge |
author_sort | Sun, Cheng |
collection | PubMed |
description | BACKGROUND: Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 – 75 Gb, 12–74 Gb of which are lost from pre-somatic cell lineages at germline – soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. RESULTS: Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. CONCLUSIONS: Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms. |
format | Online Article Text |
id | pubmed-4029161 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40291612014-05-22 Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development Sun, Cheng Wyngaard, Grace Walton, D Brian Wichman, Holly A Mueller, Rachel Lockridge BMC Genomics Research Article BACKGROUND: Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 – 75 Gb, 12–74 Gb of which are lost from pre-somatic cell lineages at germline – soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. RESULTS: Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. CONCLUSIONS: Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms. BioMed Central 2014-03-11 /pmc/articles/PMC4029161/ /pubmed/24618421 http://dx.doi.org/10.1186/1471-2164-15-186 Text en Copyright © 2014 Sun et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Research Article Sun, Cheng Wyngaard, Grace Walton, D Brian Wichman, Holly A Mueller, Rachel Lockridge Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title | Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title_full | Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title_fullStr | Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title_full_unstemmed | Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title_short | Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
title_sort | billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029161/ https://www.ncbi.nlm.nih.gov/pubmed/24618421 http://dx.doi.org/10.1186/1471-2164-15-186 |
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