Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar
Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high...
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| Veröffentlicht in: | Nature genetics 2022-03, Vol.54 (3), p.342-348 |
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| creator | Sun, Hequan Jiao, Wen-Biao Krause, Kristin Campoy, José A. Goel, Manish Folz-Donahue, Kat Kukat, Christian Huettel, Bruno Schneeberger, Korbinian |
| description | Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.
Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding. |
| doi_str_mv | 10.1038/s41588-022-01015-0 |
| format | Article |
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Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/s41588-022-01015-0</identifier><identifier>PMID: 35241824</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/114/2785 ; 631/208/212 ; 631/449/711 ; 631/61/212/2302 ; Accuracy ; Agriculture ; Alleles ; Animal Genetics and Genomics ; Assembly ; Autotetraploid ; Biomedical and Life Sciences ; Biomedicine ; Cancer Research ; Chromosomes ; Cultivars ; DNA methylation ; Functional morphology ; Gene Function ; Genes ; Genomes ; Genomics ; Haplotypes ; Haplotypes - genetics ; Human Genetics ; Inbreeding ; Plant Breeding ; Pollen ; Potatoes ; Ribosomal DNA ; Solanum tuberosum - genetics ; Tetraploidy ; Transcriptomes ; Vegetables</subject><ispartof>Nature genetics, 2022-03, Vol.54 (3), p.342-348</ispartof><rights>The Author(s) 2022</rights><rights>2022. The Author(s).</rights><rights>Copyright Nature Publishing Group Mar 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c540t-a7e4e602cdf712142a92e59cb727de053b0179e71ba593268c21a3555165f433</citedby><cites>FETCH-LOGICAL-c540t-a7e4e602cdf712142a92e59cb727de053b0179e71ba593268c21a3555165f433</cites><orcidid>0000-0001-9908-7035 ; 0000-0002-5512-0443 ; 0000-0003-2046-2109 ; 0000-0002-6087-6990 ; 0000-0003-1508-0229 ; 0000-0001-8355-2959</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,315,782,786,887,27931,27932</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35241824$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Hequan</creatorcontrib><creatorcontrib>Jiao, Wen-Biao</creatorcontrib><creatorcontrib>Krause, Kristin</creatorcontrib><creatorcontrib>Campoy, José A.</creatorcontrib><creatorcontrib>Goel, Manish</creatorcontrib><creatorcontrib>Folz-Donahue, Kat</creatorcontrib><creatorcontrib>Kukat, Christian</creatorcontrib><creatorcontrib>Huettel, Bruno</creatorcontrib><creatorcontrib>Schneeberger, Korbinian</creatorcontrib><title>Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar</title><title>Nature genetics</title><addtitle>Nat Genet</addtitle><addtitle>Nat Genet</addtitle><description>Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.
Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding.</description><subject>631/114/2785</subject><subject>631/208/212</subject><subject>631/449/711</subject><subject>631/61/212/2302</subject><subject>Accuracy</subject><subject>Agriculture</subject><subject>Alleles</subject><subject>Animal Genetics and Genomics</subject><subject>Assembly</subject><subject>Autotetraploid</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Chromosomes</subject><subject>Cultivars</subject><subject>DNA methylation</subject><subject>Functional morphology</subject><subject>Gene Function</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Human Genetics</subject><subject>Inbreeding</subject><subject>Plant Breeding</subject><subject>Pollen</subject><subject>Potatoes</subject><subject>Ribosomal DNA</subject><subject>Solanum tuberosum - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Hequan</au><au>Jiao, Wen-Biao</au><au>Krause, Kristin</au><au>Campoy, José A.</au><au>Goel, Manish</au><au>Folz-Donahue, Kat</au><au>Kukat, Christian</au><au>Huettel, Bruno</au><au>Schneeberger, Korbinian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2022-03-01</date><risdate>2022</risdate><volume>54</volume><issue>3</issue><spage>342</spage><epage>348</epage><pages>342-348</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><abstract>Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.
Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>35241824</pmid><doi>10.1038/s41588-022-01015-0</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0001-9908-7035</orcidid><orcidid>https://orcid.org/0000-0002-5512-0443</orcidid><orcidid>https://orcid.org/0000-0003-2046-2109</orcidid><orcidid>https://orcid.org/0000-0002-6087-6990</orcidid><orcidid>https://orcid.org/0000-0003-1508-0229</orcidid><orcidid>https://orcid.org/0000-0001-8355-2959</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 631/114/2785 631/208/212 631/449/711 631/61/212/2302 Accuracy Agriculture Alleles Animal Genetics and Genomics Assembly Autotetraploid Biomedical and Life Sciences Biomedicine Cancer Research Chromosomes Cultivars DNA methylation Functional morphology Gene Function Genes Genomes Genomics Haplotypes Haplotypes - genetics Human Genetics Inbreeding Plant Breeding Pollen Potatoes Ribosomal DNA Solanum tuberosum - genetics Tetraploidy Transcriptomes Vegetables |
| title | Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar |
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