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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

View ORCID ProfileHarmeet Singh Chawla, View ORCID ProfileHueyTyng Lee, Iulian Gabur, Suriya Tamilselvan-Nattar-Amutha, View ORCID ProfileChristian Obermeier, View ORCID ProfileSarah V. Schiessl, Jia-Ming Song, View ORCID ProfileKede Liu, View ORCID ProfileLiang Guo, View ORCID ProfileIsobel A. P. Parkin, View ORCID ProfileRod J. Snowdon
doi: https://doi.org/10.1101/2020.01.27.915470
Harmeet Singh Chawla
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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HueyTyng Lee
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Iulian Gabur
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Suriya Tamilselvan-Nattar-Amutha
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Christian Obermeier
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Sarah V. Schiessl
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Jia-Ming Song
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Kede Liu
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Liang Guo
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Isobel A. P. Parkin
Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
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Rod J. Snowdon
Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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  • For correspondence: rod.snowdon@agrar.uni-giessen.de
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Summary

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

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Posted January 28, 2020.
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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
Harmeet Singh Chawla, HueyTyng Lee, Iulian Gabur, Suriya Tamilselvan-Nattar-Amutha, Christian Obermeier, Sarah V. Schiessl, Jia-Ming Song, Kede Liu, Liang Guo, Isobel A. P. Parkin, Rod J. Snowdon
bioRxiv 2020.01.27.915470; doi: https://doi.org/10.1101/2020.01.27.915470
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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
Harmeet Singh Chawla, HueyTyng Lee, Iulian Gabur, Suriya Tamilselvan-Nattar-Amutha, Christian Obermeier, Sarah V. Schiessl, Jia-Ming Song, Kede Liu, Liang Guo, Isobel A. P. Parkin, Rod J. Snowdon
bioRxiv 2020.01.27.915470; doi: https://doi.org/10.1101/2020.01.27.915470

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