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Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

View ORCID ProfileAurélie Canaguier, Romane Guilbaud, View ORCID ProfileErwan Denis, Ghislaine Magdelenat, View ORCID ProfileCaroline Belser, View ORCID ProfileBenjamin Istace, View ORCID ProfileCorinne Cruaud, View ORCID ProfilePatrick Wincker, View ORCID ProfileMarie-Christine Le Paslier, Patricia Faivre-Rampant, View ORCID ProfileValérie Barbe
doi: https://doi.org/10.1101/2021.04.16.440130
Aurélie Canaguier
1Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000, Evry-Courcouronnes, France
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  • ORCID record for Aurélie Canaguier
Romane Guilbaud
1Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000, Evry-Courcouronnes, France
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Erwan Denis
3Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
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Ghislaine Magdelenat
3Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
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Caroline Belser
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Benjamin Istace
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Corinne Cruaud
3Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
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  • ORCID record for Corinne Cruaud
Patrick Wincker
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Marie-Christine Le Paslier
1Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000, Evry-Courcouronnes, France
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Patricia Faivre-Rampant
1Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000, Evry-Courcouronnes, France
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  • For correspondence: patricia.faivre-rampant@inrae.fr
Valérie Barbe
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Abstract

Background Structural Variations (SVs) are very diverse genomic rearrangements. In the past, their detection was restricted to cytological approaches, then to NGS read size and partitionned assemblies. Due to the current capabilities of technologies such as long read sequencing and optical mapping, larger SVs detection are becoming more and more accessible.

This study proposes a comparison in SVs detection and characterization from long-read sequencing obtained with the MinION device developed by Oxford Nanopore Technologies and from optical mapping produced by the Saphyr device commercialized by Bionano Genomics. The genomes of the two Arabidopsis thaliana ecotypes Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1) were chosen to guide the use of one or the other technology.

Results We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 on the public reference Col-0 TAIR10.1. After filtering, 1 184 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 in both technologies. 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, most of detected SVs were found in same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the later being more efficient to characterize large SVs. Even if both technologies are obvious complementary approaches, ONT data appears to be more adapted to large scale populations study, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • aurelie.canaguier{at}inrae.fr, romane.guilbaud{at}inrae.fr, erwandenis{at}hotmail.com, gmagdele{at}genoscope.cns.fr, cbelser{at}genoscope.cns.fr, bistace{at}genoscope.cns.fr, cruaud{at}genoscope.cns.fr, marie-christine.le-paslier{at}inrae.fr, pwincker{at}genoscope.cns.fr, vbarbe{at}genoscope.cns.fr

  • List of abbreviations

    bp
    base pairs
    BRK
    Break
    CGH
    Comparative Genomic Hybridization
    CNV
    copy number variations
    Col-0
    Arabidopsis thaliana ecotypes Columbia-0
    DEL
    Deletion
    DLE-1
    Direct Label Enzyme – 1
    DLS
    Direct Label and Stain
    DNA
    Desoxyribo Nucleic Acid
    DUP
    Duplication
    Gb
    Gigabases
    Hi-C
    HIgh-throughput chromatin conformation Capture
    Indels insertions/deletions
    INS
    Insertion
    INV
    Inversion
    JMP
    Jump
    Kb
    kilobases
    Ler-1
    Arabidopsis thaliana ecotypes Landsberg erecta 1
    LER
    Arabdopsis thaliana Ler-1 reference genome published by Zapata et al. 2016
    NA
    Not Available
    NGS
    Next Generation Sequence
    ONT
    Oxford Nanopore Technologies
    PAV
    presence/absence variations
    RA
    Rapid Assembler
    SDN
    SMARTdenovo
    SEQ
    Sequence
    SNP
    Single Nucleotid Polymorphism
    SV
    Structural Variation
    TAIR10.1
    last version of Arabdopsis thaliana Col-0 reference genome availbale at the The Arabidopsis Information Resource repository (TAIR)
    TE
    Transposable Element
    TRA
    Translocation
  • Copyright 
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    Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection
    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
    bioRxiv 2021.04.16.440130; doi: https://doi.org/10.1101/2021.04.16.440130
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    Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection
    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
    bioRxiv 2021.04.16.440130; doi: https://doi.org/10.1101/2021.04.16.440130

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