Cargando…

Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species

Transposons are mobile DNA elements that generate both adaptive and deleterious phenotypic variation thereby driving genome evolution. For these reasons, genomes have mechanisms to regulate transposable element (TE) activity. Approximately 12–16% of the Caenorhabditis elegans genome is composed of T...

Descripción completa

Detalles Bibliográficos
Autores principales: Laricchia, K.M., Zdraljevic, S., Cook, D.E., Andersen, E.C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850821/
https://www.ncbi.nlm.nih.gov/pubmed/28486636
http://dx.doi.org/10.1093/molbev/msx155
_version_ 1783306290821332992
author Laricchia, K.M.
Zdraljevic, S.
Cook, D.E.
Andersen, E.C.
author_facet Laricchia, K.M.
Zdraljevic, S.
Cook, D.E.
Andersen, E.C.
author_sort Laricchia, K.M.
collection PubMed
description Transposons are mobile DNA elements that generate both adaptive and deleterious phenotypic variation thereby driving genome evolution. For these reasons, genomes have mechanisms to regulate transposable element (TE) activity. Approximately 12–16% of the Caenorhabditis elegans genome is composed of TEs, of which the majority are likely inactive. However, most studies of TE activity have been conducted in the laboratory strain N2, which limits our knowledge of the effects of these mobile elements across natural populations. We analyzed the distribution and abundance of TEs in 208 wild C. elegans strains to better understand how transposons contribute to variation in natural populations. We identified 3,397 TEs as compared with the reference strain, of which 2,771 are novel insertions and 241 are TEs that have been excised in at least one wild strain. Likely because of their hypothesized deleterious effects, we find that TEs are found at low allele frequencies throughout the population, and we predict functional effects of TE insertions. The abundances of TEs reflect their activities, and these data allowed us to perform both genome-wide association mappings and rare variant correlations to reveal several candidate genes that impact TE regulation, including small regulatory piwi-interacting RNAs and chromatin factors. Because TE variation in natural populations could underlie phenotypic variation for organismal and behavioral traits, the transposons that we identified and their regulatory mechanisms can be used in future studies to explore the genomics of complex traits and evolutionary changes.
format Online
Article
Text
id pubmed-5850821
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-58508212018-03-23 Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species Laricchia, K.M. Zdraljevic, S. Cook, D.E. Andersen, E.C. Mol Biol Evol Discoveries Transposons are mobile DNA elements that generate both adaptive and deleterious phenotypic variation thereby driving genome evolution. For these reasons, genomes have mechanisms to regulate transposable element (TE) activity. Approximately 12–16% of the Caenorhabditis elegans genome is composed of TEs, of which the majority are likely inactive. However, most studies of TE activity have been conducted in the laboratory strain N2, which limits our knowledge of the effects of these mobile elements across natural populations. We analyzed the distribution and abundance of TEs in 208 wild C. elegans strains to better understand how transposons contribute to variation in natural populations. We identified 3,397 TEs as compared with the reference strain, of which 2,771 are novel insertions and 241 are TEs that have been excised in at least one wild strain. Likely because of their hypothesized deleterious effects, we find that TEs are found at low allele frequencies throughout the population, and we predict functional effects of TE insertions. The abundances of TEs reflect their activities, and these data allowed us to perform both genome-wide association mappings and rare variant correlations to reveal several candidate genes that impact TE regulation, including small regulatory piwi-interacting RNAs and chromatin factors. Because TE variation in natural populations could underlie phenotypic variation for organismal and behavioral traits, the transposons that we identified and their regulatory mechanisms can be used in future studies to explore the genomics of complex traits and evolutionary changes. Oxford University Press 2017-09 2017-05-09 /pmc/articles/PMC5850821/ /pubmed/28486636 http://dx.doi.org/10.1093/molbev/msx155 Text en © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Discoveries
Laricchia, K.M.
Zdraljevic, S.
Cook, D.E.
Andersen, E.C.
Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title_full Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title_fullStr Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title_full_unstemmed Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title_short Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species
title_sort natural variation in the distribution and abundance of transposable elements across the caenorhabditis elegans species
topic Discoveries
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850821/
https://www.ncbi.nlm.nih.gov/pubmed/28486636
http://dx.doi.org/10.1093/molbev/msx155
work_keys_str_mv AT laricchiakm naturalvariationinthedistributionandabundanceoftransposableelementsacrossthecaenorhabditiselegansspecies
AT zdraljevics naturalvariationinthedistributionandabundanceoftransposableelementsacrossthecaenorhabditiselegansspecies
AT cookde naturalvariationinthedistributionandabundanceoftransposableelementsacrossthecaenorhabditiselegansspecies
AT andersenec naturalvariationinthedistributionandabundanceoftransposableelementsacrossthecaenorhabditiselegansspecies