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Discovery and population genomics of structural variation in a songbird genus
Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = ...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341801/ https://www.ncbi.nlm.nih.gov/pubmed/32636372 http://dx.doi.org/10.1038/s41467-020-17195-4 |
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author | Weissensteiner, Matthias H. Bunikis, Ignas Catalán, Ana Francoijs, Kees-Jan Knief, Ulrich Heim, Wieland Peona, Valentina Pophaly, Saurabh D. Sedlazeck, Fritz J. Suh, Alexander Warmuth, Vera M. Wolf, Jochen B. W. |
author_facet | Weissensteiner, Matthias H. Bunikis, Ignas Catalán, Ana Francoijs, Kees-Jan Knief, Ulrich Heim, Wieland Peona, Valentina Pophaly, Saurabh D. Sedlazeck, Fritz J. Suh, Alexander Warmuth, Vera M. Wolf, Jochen B. W. |
author_sort | Weissensteiner, Matthias H. |
collection | PubMed |
description | Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping. |
format | Online Article Text |
id | pubmed-7341801 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-73418012020-07-09 Discovery and population genomics of structural variation in a songbird genus Weissensteiner, Matthias H. Bunikis, Ignas Catalán, Ana Francoijs, Kees-Jan Knief, Ulrich Heim, Wieland Peona, Valentina Pophaly, Saurabh D. Sedlazeck, Fritz J. Suh, Alexander Warmuth, Vera M. Wolf, Jochen B. W. Nat Commun Article Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping. Nature Publishing Group UK 2020-07-07 /pmc/articles/PMC7341801/ /pubmed/32636372 http://dx.doi.org/10.1038/s41467-020-17195-4 Text en © The Author(s) 2020, corrected publication 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Weissensteiner, Matthias H. Bunikis, Ignas Catalán, Ana Francoijs, Kees-Jan Knief, Ulrich Heim, Wieland Peona, Valentina Pophaly, Saurabh D. Sedlazeck, Fritz J. Suh, Alexander Warmuth, Vera M. Wolf, Jochen B. W. Discovery and population genomics of structural variation in a songbird genus |
title | Discovery and population genomics of structural variation in a songbird genus |
title_full | Discovery and population genomics of structural variation in a songbird genus |
title_fullStr | Discovery and population genomics of structural variation in a songbird genus |
title_full_unstemmed | Discovery and population genomics of structural variation in a songbird genus |
title_short | Discovery and population genomics of structural variation in a songbird genus |
title_sort | discovery and population genomics of structural variation in a songbird genus |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341801/ https://www.ncbi.nlm.nih.gov/pubmed/32636372 http://dx.doi.org/10.1038/s41467-020-17195-4 |
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