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High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

Tiange Lang, Pierre Abadie, Valérie Léger, Thibaut Decourcelle, Jean-Marc Frigerio, Christian Burban, Catherine Bodénès, Erwan Guichoux, Grégoire Le Provost, Cécile Robin, Naoki Tani, Patrick Léger, Camille Lepoittevin, Veronica A. El Mujtar, François Hubert, Josquin Tibbits, Jorge Paiva, Alain Franc, Frédéric Raspail, Stéphanie Mariette, Marie-Pierre Reviron, Christophe Plomion, Antoine Kremer, Marie-Laure Desprez-Loustau, View ORCID ProfilePauline Garnier-Géré
doi: https://doi.org/10.1101/388447
Tiange Lang
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
3Big Data Decision Institute, Jinan University, Tianhe, Guangzhou, PR China
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Pierre Abadie
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Valérie Léger
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Thibaut Decourcelle
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
4GEVES, 25 rue Georges Morel, 49071, Beaucouzé, France
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Jean-Marc Frigerio
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Christian Burban
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Catherine Bodénès
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Erwan Guichoux
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Grégoire Le Provost
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Cécile Robin
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Naoki Tani
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
5Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
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Patrick Léger
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Camille Lepoittevin
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Veronica A. El Mujtar
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
6Unidad de Genética Ecológica y Mejoramiento Forestal. Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Bariloche, Modesta Victoria 4450 (8400), Bariloche, Río Negro, Argentina
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François Hubert
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Josquin Tibbits
7Department of Environment and Primary Industries, Biosciences Research Division, Agribio, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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Jorge Paiva
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
8Instituto de Biologia Experimental e Tecnologica, iBET, Apartado 12, Oeiras 2780-901, Portugal
9Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska street, Poznan PL-60-479, Poland
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Alain Franc
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Frédéric Raspail
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Stéphanie Mariette
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Marie-Pierre Reviron
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Christophe Plomion
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Antoine Kremer
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Marie-Laure Desprez-Loustau
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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Pauline Garnier-Géré
1INRAE, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France
2Univ. Bordeaux, UMR 1202, Biodiversity Genes & Communities, F-33400 Talence, France
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  • ORCID record for Pauline Garnier-Géré
  • For correspondence: pauline.garnier-gere@inrae.fr
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Abstract

In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Cite as: Lang, T., Abadie, P., Léger, V., Decourcelle, T., Frigerio, J.-M., Burban, C., Bodénès, C., Guichoux, E., Le Provost, G., Robin, C., Tani, N., Léger, P., Lepoittevin, C., El Mujtar, V. A., Hubert, F., Tibbits, J., Paiva, J., Franc, A., Raspail, F., Mariette, S., Reviron, M.-P., Plomion, C., Kremer, A., Desprez-Loustau, M.-L. and Garnier-Géré, P. (2021). High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur). bioRxiv, 388447, ver. 4 peer-reviewed and recommended by PCI Forest and Wood Sciences. doi: https://doi.org/10.1101/388447

  • This article has been peer-reviewed and recommended by Peer Community in Forest & Wood Sciences https://doi.org/10.24072/pci.forestwoodsci.100003

  • Version 4 of this preprint has been peer-reviewed and recommended by Peer Community In Forest and Wood Sciences (https://doi.org/10.24072/pci.forestwoodsci.100003)

  • https://github.com/garniergere/Reference.Db.SNPs.Quercus

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)
Tiange Lang, Pierre Abadie, Valérie Léger, Thibaut Decourcelle, Jean-Marc Frigerio, Christian Burban, Catherine Bodénès, Erwan Guichoux, Grégoire Le Provost, Cécile Robin, Naoki Tani, Patrick Léger, Camille Lepoittevin, Veronica A. El Mujtar, François Hubert, Josquin Tibbits, Jorge Paiva, Alain Franc, Frédéric Raspail, Stéphanie Mariette, Marie-Pierre Reviron, Christophe Plomion, Antoine Kremer, Marie-Laure Desprez-Loustau, Pauline Garnier-Géré
bioRxiv 388447; doi: https://doi.org/10.1101/388447
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High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)
Tiange Lang, Pierre Abadie, Valérie Léger, Thibaut Decourcelle, Jean-Marc Frigerio, Christian Burban, Catherine Bodénès, Erwan Guichoux, Grégoire Le Provost, Cécile Robin, Naoki Tani, Patrick Léger, Camille Lepoittevin, Veronica A. El Mujtar, François Hubert, Josquin Tibbits, Jorge Paiva, Alain Franc, Frédéric Raspail, Stéphanie Mariette, Marie-Pierre Reviron, Christophe Plomion, Antoine Kremer, Marie-Laure Desprez-Loustau, Pauline Garnier-Géré
bioRxiv 388447; doi: https://doi.org/10.1101/388447

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