Low-pass nanopore sequencing for measurement of global methylation levels in plants
Abstract Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low-pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-11145-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846101430290612224 |
|---|---|
| author | Yusmiati Liau Annabel Whibley Amy M. Hill Bhanupratap R. Vanga Meeghan Pither-Joyce Elena Hilario Sarah Bailey Susan J. Thomson Darrell Lizamore |
| author_facet | Yusmiati Liau Annabel Whibley Amy M. Hill Bhanupratap R. Vanga Meeghan Pither-Joyce Elena Hilario Sarah Bailey Susan J. Thomson Darrell Lizamore |
| author_sort | Yusmiati Liau |
| collection | DOAJ |
| description | Abstract Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low-pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that higher coverage (0.1x) is required to achieve accuracy in assessing plant global methylation comparable to that in vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns were observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses, and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements. |
| format | Article |
| id | doaj-art-ad7f9739faa44056b1e511f3d42a0e07 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-ad7f9739faa44056b1e511f3d42a0e072024-12-29T12:10:56ZengBMCBMC Genomics1471-21642024-12-0125111210.1186/s12864-024-11145-wLow-pass nanopore sequencing for measurement of global methylation levels in plantsYusmiati Liau0Annabel Whibley1Amy M. Hill2Bhanupratap R. Vanga3Meeghan Pither-Joyce4Elena Hilario5Sarah Bailey6Susan J. Thomson7Darrell Lizamore8Grapevine Improvement, Bragato Research InstituteGrapevine Improvement, Bragato Research InstituteGrapevine Improvement, Bragato Research InstituteGrapevine Improvement, Bragato Research InstituteThe New Zealand Institute for Plant and Food Research LimitedLincoln UniversityLincoln UniversityThe New Zealand Institute for Plant and Food Research LimitedGrapevine Improvement, Bragato Research InstituteAbstract Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low-pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that higher coverage (0.1x) is required to achieve accuracy in assessing plant global methylation comparable to that in vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns were observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses, and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements.https://doi.org/10.1186/s12864-024-11145-wNanopore methylation sequencingSkimseqPlantVitis vinifera |
| spellingShingle | Yusmiati Liau Annabel Whibley Amy M. Hill Bhanupratap R. Vanga Meeghan Pither-Joyce Elena Hilario Sarah Bailey Susan J. Thomson Darrell Lizamore Low-pass nanopore sequencing for measurement of global methylation levels in plants BMC Genomics Nanopore methylation sequencing Skimseq Plant Vitis vinifera |
| title | Low-pass nanopore sequencing for measurement of global methylation levels in plants |
| title_full | Low-pass nanopore sequencing for measurement of global methylation levels in plants |
| title_fullStr | Low-pass nanopore sequencing for measurement of global methylation levels in plants |
| title_full_unstemmed | Low-pass nanopore sequencing for measurement of global methylation levels in plants |
| title_short | Low-pass nanopore sequencing for measurement of global methylation levels in plants |
| title_sort | low pass nanopore sequencing for measurement of global methylation levels in plants |
| topic | Nanopore methylation sequencing Skimseq Plant Vitis vinifera |
| url | https://doi.org/10.1186/s12864-024-11145-w |
| work_keys_str_mv | AT yusmiatiliau lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT annabelwhibley lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT amymhill lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT bhanuprataprvanga lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT meeghanpitherjoyce lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT elenahilario lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT sarahbailey lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT susanjthomson lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants AT darrelllizamore lowpassnanoporesequencingformeasurementofglobalmethylationlevelsinplants |