Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Abstract Background The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3936-7 |
| _version_ | 1828182641479778304 |
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| author | Michael Giolai Pirita Paajanen Walter Verweij Kamil Witek Jonathan D. G. Jones Matthew D. Clark |
| author_facet | Michael Giolai Pirita Paajanen Walter Verweij Kamil Witek Jonathan D. G. Jones Matthew D. Clark |
| author_sort | Michael Giolai |
| collection | DOAJ |
| description | Abstract Background The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. Results Sequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn’t generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline. Conclusion The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project. |
| first_indexed | 2024-04-12T06:21:28Z |
| format | Article |
| id | doaj.art-7700d204a937401aa938186f72997faa |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T06:21:28Z |
| publishDate | 2017-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7700d204a937401aa938186f72997faa2022-12-22T03:44:17ZengBMCBMC Genomics1471-21642017-07-0118111510.1186/s12864-017-3936-7Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoireMichael Giolai0Pirita Paajanen1Walter Verweij2Kamil Witek3Jonathan D. G. Jones4Matthew D. Clark5Earlham Institute (EI)Earlham Institute (EI)Earlham Institute (EI)The Sainsbury LaboratoryThe Sainsbury LaboratoryEarlham Institute (EI)Abstract Background The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. Results Sequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn’t generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline. Conclusion The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project.http://link.springer.com/article/10.1186/s12864-017-3936-7Targeted captureGene enrichmentOxford Nanopore technologiesMinIONPacBioRenSeq |
| spellingShingle | Michael Giolai Pirita Paajanen Walter Verweij Kamil Witek Jonathan D. G. Jones Matthew D. Clark Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire BMC Genomics Targeted capture Gene enrichment Oxford Nanopore technologies MinION PacBio RenSeq |
| title | Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire |
| title_full | Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire |
| title_fullStr | Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire |
| title_full_unstemmed | Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire |
| title_short | Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire |
| title_sort | comparative analysis of targeted long read sequencing approaches for characterization of a plant s immune receptor repertoire |
| topic | Targeted capture Gene enrichment Oxford Nanopore technologies MinION PacBio RenSeq |
| url | http://link.springer.com/article/10.1186/s12864-017-3936-7 |
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