Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

Manyara, David; Sánchez-García, Marisol; Montoliu-Nerin, Merce; Rosling, Anna; European Commission

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

11 Pág.

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Main Authors:	Manyara, David, Sánchez-García, Marisol, Montoliu-Nerin, Merce, Rosling, Anna
Other Authors:	European Commission
Format:	artículo biblioteca
Language:	English
Published:	Genetics Society of America 2024-04-24
Subjects:	AM fungi, SNP calling, Intraorganismal variation, Low-frequency variants, Pooled samples, Pooled spores and mycelia, Single nuclei, Single spore,
Online Access:	http://hdl.handle.net/10261/361978 http://dx.doi.org/10.13039/501100000780 https://api.elsevier.com/content/abstract/scopus_id/85195328161
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id	dig-inia-es-10261-361978
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spelling	dig-inia-es-10261-3619782024-10-26T20:47:59Z Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198 Manyara, David Sánchez-García, Marisol Montoliu-Nerin, Merce Rosling, Anna European Commission Swedish Research Council Manyara, David [0000-0002-8370-2651] Sánchez-García, Marisol [0000-0002-0635-6281] Montoliu-Nerin, Merce [0000-0002-5200-0411] Rosling, Anna [0000-0002-7003-5941] Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore 11 Pág. Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi. This study was funded by the European Research Council under the project number 678792. Computational analyses were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through UPPMAX, partially funded by the Swedish Research Council through grant agreement no. 2018-05973. The paper was greatly improved thanks to constructive comments from 2 anonymous reviewers in G3. Peer reviewed 2024-06-28T07:06:31Z 2024-06-28T07:06:31Z 2024-04-24 artículo http://purl.org/coar/resource_type/c_6501 G3 genes - genomes - genetics 14(6): jkae074 (2024) http://hdl.handle.net/10261/361978 10.1093/g3journal/jkae074 2160-1836 http://dx.doi.org/10.13039/501100000780 38656424 2-s2.0-85195328161 https://api.elsevier.com/content/abstract/scopus_id/85195328161 en #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/678792 Centro de Biotecnología y Genómica de Plantas (CBGP) Publisher's version https://doi.org/10.1093/g3journal/jkae074 Sí open application/pdf Genetics Society of America
institution	INIA ES
collection	DSpace
country	España
countrycode	ES
component	Bibliográfico
access	En linea
databasecode	dig-inia-es
tag	biblioteca
region	Europa del Sur
libraryname	Biblioteca del INIA España
language	English
topic	AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore
spellingShingle	AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore Manyara, David Sánchez-García, Marisol Montoliu-Nerin, Merce Rosling, Anna Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
description	11 Pág.
author2	European Commission
author_facet	European Commission Manyara, David Sánchez-García, Marisol Montoliu-Nerin, Merce Rosling, Anna
format	artículo
topic_facet	AM fungi SNP calling Intraorganismal variation Low-frequency variants Pooled samples Pooled spores and mycelia Single nuclei Single spore
author	Manyara, David Sánchez-García, Marisol Montoliu-Nerin, Merce Rosling, Anna
author_sort	Manyara, David
title	Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
title_short	Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
title_full	Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
title_fullStr	Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
title_full_unstemmed	Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
title_sort	detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species rhizophagus irregularis daom197198
publisher	Genetics Society of America
publishDate	2024-04-24
url	http://hdl.handle.net/10261/361978 http://dx.doi.org/10.13039/501100000780 https://api.elsevier.com/content/abstract/scopus_id/85195328161
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Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

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