Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198
11 Pág.
Saved in:
| Main Authors: | , , , |
|---|---|
| Other Authors: | |
| 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 https://api.elsevier.com/content/abstract/scopus_id/85195328161 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| id |
dig-inia-es-10261-361978 |
|---|---|
| record_format |
koha |
| spelling |
dig-inia-es-10261-3619782024-06-28T20:36:33Z 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] 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 G3 genes - genomes - genetics 14(6): jkae074 (2024) http://hdl.handle.net/10261/361978 10.1093/g3journal/jkae074 2160-1836 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 https://api.elsevier.com/content/abstract/scopus_id/85195328161 |
| work_keys_str_mv |
AT manyaradavid detectionofrarevariantsamongnucleipopulatingthearbuscularmycorrhizalfungalmodelspeciesrhizophagusirregularisdaom197198 AT sanchezgarciamarisol detectionofrarevariantsamongnucleipopulatingthearbuscularmycorrhizalfungalmodelspeciesrhizophagusirregularisdaom197198 AT montoliunerinmerce detectionofrarevariantsamongnucleipopulatingthearbuscularmycorrhizalfungalmodelspeciesrhizophagusirregularisdaom197198 AT roslinganna detectionofrarevariantsamongnucleipopulatingthearbuscularmycorrhizalfungalmodelspeciesrhizophagusirregularisdaom197198 |
| _version_ |
1807153710724284416 |