Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping
We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions co...
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doaj-9c8e8b0769cb40409eace8aec6cb468e2020-11-24T20:58:13ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-07-01910.3389/fpls.2018.00971341148Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical MappingYuxuan Yuan0Yuxuan Yuan1Zbyněk Milec2Philipp E. Bayer3Philipp E. Bayer4Jan Vrána5Jaroslav Doležel6David Edwards7David Edwards8William Erskine9William Erskine10Parwinder Kaur11Parwinder Kaur12Parwinder Kaur13School of Biological Sciences, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CzechiaSchool of Biological Sciences, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CzechiaInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CzechiaSchool of Biological Sciences, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaTelethon Kids Institute, Perth, WA, AustraliaWe selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.https://www.frontiersin.org/article/10.3389/fpls.2018.00971/fullstructural variationoptical mappingBionanonucleotide validationreference |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yuxuan Yuan Yuxuan Yuan Zbyněk Milec Philipp E. Bayer Philipp E. Bayer Jan Vrána Jaroslav Doležel David Edwards David Edwards William Erskine William Erskine Parwinder Kaur Parwinder Kaur Parwinder Kaur |
spellingShingle |
Yuxuan Yuan Yuxuan Yuan Zbyněk Milec Philipp E. Bayer Philipp E. Bayer Jan Vrána Jaroslav Doležel David Edwards David Edwards William Erskine William Erskine Parwinder Kaur Parwinder Kaur Parwinder Kaur Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping Frontiers in Plant Science structural variation optical mapping Bionano nucleotide validation reference |
author_facet |
Yuxuan Yuan Yuxuan Yuan Zbyněk Milec Philipp E. Bayer Philipp E. Bayer Jan Vrána Jaroslav Doležel David Edwards David Edwards William Erskine William Erskine Parwinder Kaur Parwinder Kaur Parwinder Kaur |
author_sort |
Yuxuan Yuan |
title |
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping |
title_short |
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping |
title_full |
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping |
title_fullStr |
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping |
title_full_unstemmed |
Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping |
title_sort |
large-scale structural variation detection in subterranean clover subtypes using optical mapping |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2018-07-01 |
description |
We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases. |
topic |
structural variation optical mapping Bionano nucleotide validation reference |
url |
https://www.frontiersin.org/article/10.3389/fpls.2018.00971/full |
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