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Large structural variations in the haplotype‐resolved African cassava genome.

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Title: Large structural variations in the haplotype‐resolved African cassava genome.
Authors: Mansfeld, Ben N.1 (AUTHOR), Boyher, Adam1 (AUTHOR), Berry, Jeffrey C.1 (AUTHOR), Wilson, Mark1 (AUTHOR), Ou, Shujun2 (AUTHOR), Polydore, Seth1 (AUTHOR), Michael, Todd P.3 (AUTHOR), Fahlgren, Noah1 (AUTHOR), Bart, Rebecca S.1 (AUTHOR) rbart@danforthcenter.org
Source: Plant Journal. Dec2021, Vol. 108 Issue 6, p1830-1848. 19p.
Subjects: Haplotypes, Genetic load, Cassava, Botany, Genomes, Genetic variation
Geographic Terms: Africa
Abstract: Summary: Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype‐dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi‐C to resolve each haplotype of the genome of a farmer‐preferred cassava line, TME7 (Oko‐iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON‐Phase and Hi‐C read data. The ultralong‐range information from Hi‐C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype‐specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele‐specific expression was further explored. RNA‐sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy‐to‐use web‐based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype‐specific structural variation, gene hemizygosity, and allele‐specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava. Significance Statement: The cassava varieties grown by subsistence farmers in Africa largely differ from the partially inbred reference genome due to their highly heterozygous nature. We used multiple sequencing technologies to assemble and resolve both haplotypes in TME7, a farmer‐preferred cassava line, enabling us to study the considerable haplotypic structural variation in this line. [ABSTRACT FROM AUTHOR]
Copyright of Plant Journal is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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  Data: Large structural variations in the haplotype‐resolved African cassava genome.
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  Data: <searchLink fieldCode="AR" term="%22Mansfeld%2C+Ben+N%2E%22">Mansfeld, Ben N.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Boyher%2C+Adam%22">Boyher, Adam</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Berry%2C+Jeffrey+C%2E%22">Berry, Jeffrey C.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Wilson%2C+Mark%22">Wilson, Mark</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ou%2C+Shujun%22">Ou, Shujun</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Polydore%2C+Seth%22">Polydore, Seth</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Michael%2C+Todd+P%2E%22">Michael, Todd P.</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Fahlgren%2C+Noah%22">Fahlgren, Noah</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Bart%2C+Rebecca+S%2E%22">Bart, Rebecca S.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> rbart@danforthcenter.org</i>
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  Data: Summary: Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype‐dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi‐C to resolve each haplotype of the genome of a farmer‐preferred cassava line, TME7 (Oko‐iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON‐Phase and Hi‐C read data. The ultralong‐range information from Hi‐C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype‐specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele‐specific expression was further explored. RNA‐sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy‐to‐use web‐based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype‐specific structural variation, gene hemizygosity, and allele‐specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava. Significance Statement: The cassava varieties grown by subsistence farmers in Africa largely differ from the partially inbred reference genome due to their highly heterozygous nature. We used multiple sequencing technologies to assemble and resolve both haplotypes in TME7, a farmer‐preferred cassava line, enabling us to study the considerable haplotypic structural variation in this line. [ABSTRACT FROM AUTHOR]
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  Label:
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  Data: <i>Copyright of Plant Journal is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1111/tpj.15543
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      – Code: eng
        Text: English
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        PageCount: 19
        StartPage: 1830
    Subjects:
      – SubjectFull: Haplotypes
        Type: general
      – SubjectFull: Genetic load
        Type: general
      – SubjectFull: Cassava
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      – SubjectFull: Botany
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      – SubjectFull: Genomes
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      – SubjectFull: Genetic variation
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      – SubjectFull: Africa
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      – TitleFull: Large structural variations in the haplotype‐resolved African cassava genome.
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              Text: Dec2021
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