Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection
Abstract Background Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemb...
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08499-4 |
| _version_ | 1818060813803454464 |
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| author | Aurélie Canaguier Romane Guilbaud Erwan Denis Ghislaine Magdelenat Caroline Belser Benjamin Istace Corinne Cruaud Patrick Wincker Marie-Christine Le Paslier Patricia Faivre-Rampant Valérie Barbe |
| author_facet | Aurélie Canaguier Romane Guilbaud Erwan Denis Ghislaine Magdelenat Caroline Belser Benjamin Istace Corinne Cruaud Patrick Wincker Marie-Christine Le Paslier Patricia Faivre-Rampant Valérie Barbe |
| author_sort | Aurélie Canaguier |
| collection | DOAJ |
| description | Abstract Background Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1). Results We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. Conclusions Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference. |
| first_indexed | 2024-12-10T13:38:23Z |
| format | Article |
| id | doaj.art-373c746965b140e4b5f751577c9c2f6e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T13:38:23Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-373c746965b140e4b5f751577c9c2f6e2022-12-22T01:46:46ZengBMCBMC Genomics1471-21642022-04-0123111710.1186/s12864-022-08499-4Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detectionAurélie Canaguier0Romane Guilbaud1Erwan Denis2Ghislaine Magdelenat3Caroline Belser4Benjamin Istace5Corinne Cruaud6Patrick Wincker7Marie-Christine Le Paslier8Patricia Faivre-Rampant9Valérie Barbe10Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGVUniversité Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGVGenoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-SaclayGenoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-SaclayGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayGenoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-SaclayGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayUniversité Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGVUniversité Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGVGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayAbstract Background Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1). Results We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. Conclusions Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.https://doi.org/10.1186/s12864-022-08499-4Structural variationsOxford Nanopore technologiesBionano Genomics optical mappingHigh molecular weight DNAArabidopsis thaliana |
| spellingShingle | Aurélie Canaguier Romane Guilbaud Erwan Denis Ghislaine Magdelenat Caroline Belser Benjamin Istace Corinne Cruaud Patrick Wincker Marie-Christine Le Paslier Patricia Faivre-Rampant Valérie Barbe Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection BMC Genomics Structural variations Oxford Nanopore technologies Bionano Genomics optical mapping High molecular weight DNA Arabidopsis thaliana |
| title | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection |
| title_full | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection |
| title_fullStr | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection |
| title_full_unstemmed | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection |
| title_short | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection |
| title_sort | oxford nanopore and bionano genomics technologies evaluation for plant structural variation detection |
| topic | Structural variations Oxford Nanopore technologies Bionano Genomics optical mapping High molecular weight DNA Arabidopsis thaliana |
| url | https://doi.org/10.1186/s12864-022-08499-4 |
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