A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome
It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra , we generated two high-...
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| Veröffentlicht in: | Nature plants 2020-08, Vol.6 (8), p.929-941 |
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| creator | Perumal, Sampath Koh, Chu Shin Jin, Lingling Buchwaldt, Miles Higgins, Erin E. Zheng, Chunfang Sankoff, David Robinson, Stephen J. Kagale, Sateesh Navabi, Zahra-Katy Tang, Lily Horner, Kyla N. He, Zhesi Bancroft, Ian Chalhoub, Boulos Sharpe, Andrew G. Parkin, Isobel A. P. |
| description | It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed
Brassica nigra
, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events ( |
| doi_str_mv | 10.1038/s41477-020-0735-y |
| format | Article |
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Brassica nigra
, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication
Brassica-
specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating
B. nigra
from its diploid relatives.
Two high-quality nanopore genome assemblies of
Brassica nigra
are reported, one of which has particularly high contiguity with a contig N50 of 17.1 Mb, allowing localization of active centromeres and reconstruction of the ancestral
Brassica
genome.</description><identifier>ISSN: 2055-0278</identifier><identifier>EISSN: 2055-0278</identifier><identifier>DOI: 10.1038/s41477-020-0735-y</identifier><identifier>PMID: 32782408</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>45 ; 45/23 ; 45/91 ; 631/208/2491 ; 631/208/514/2254 ; Assemblies ; Biomedical and Life Sciences ; Brassica ; Brassica - genetics ; Brassica nigra ; Centromere - genetics ; Complexity ; Diploids ; DNA, Plant - genetics ; Evolution, Molecular ; Genome, Plant - genetics ; Genomes ; High-Throughput Nucleotide Sequencing ; Life Sciences ; Mathematical analysis ; Mustard Plant - genetics ; Plant Sciences</subject><ispartof>Nature plants, 2020-08, Vol.6 (8), p.929-941</ispartof><rights>Crown 2020</rights><rights>Crown 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c470t-4c7bd8fbd9c1c9e310cd622768ea52b698128b69efc0c16c2abb5074e38519f3</citedby><cites>FETCH-LOGICAL-c470t-4c7bd8fbd9c1c9e310cd622768ea52b698128b69efc0c16c2abb5074e38519f3</cites><orcidid>0000-0001-8415-5189 ; 0000-0001-8335-9876 ; 0000-0001-7707-1171 ; 0000-0002-1832-4009 ; 0000-0002-7213-1590 ; 0000-0002-5807-9466</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41477-020-0735-y$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41477-020-0735-y$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32782408$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Perumal, Sampath</creatorcontrib><creatorcontrib>Koh, Chu Shin</creatorcontrib><creatorcontrib>Jin, Lingling</creatorcontrib><creatorcontrib>Buchwaldt, Miles</creatorcontrib><creatorcontrib>Higgins, Erin E.</creatorcontrib><creatorcontrib>Zheng, Chunfang</creatorcontrib><creatorcontrib>Sankoff, David</creatorcontrib><creatorcontrib>Robinson, Stephen J.</creatorcontrib><creatorcontrib>Kagale, Sateesh</creatorcontrib><creatorcontrib>Navabi, Zahra-Katy</creatorcontrib><creatorcontrib>Tang, Lily</creatorcontrib><creatorcontrib>Horner, Kyla N.</creatorcontrib><creatorcontrib>He, Zhesi</creatorcontrib><creatorcontrib>Bancroft, Ian</creatorcontrib><creatorcontrib>Chalhoub, Boulos</creatorcontrib><creatorcontrib>Sharpe, Andrew G.</creatorcontrib><creatorcontrib>Parkin, Isobel A. P.</creatorcontrib><title>A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome</title><title>Nature plants</title><addtitle>Nat. Plants</addtitle><addtitle>Nat Plants</addtitle><description>It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed
Brassica nigra
, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication
Brassica-
specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating
B. nigra
from its diploid relatives.
Two high-quality nanopore genome assemblies of
Brassica nigra
are reported, one of which has particularly high contiguity with a contig N50 of 17.1 Mb, allowing localization of active centromeres and reconstruction of the ancestral
Brassica
genome.</description><subject>45</subject><subject>45/23</subject><subject>45/91</subject><subject>631/208/2491</subject><subject>631/208/514/2254</subject><subject>Assemblies</subject><subject>Biomedical and Life Sciences</subject><subject>Brassica</subject><subject>Brassica - genetics</subject><subject>Brassica nigra</subject><subject>Centromere - genetics</subject><subject>Complexity</subject><subject>Diploids</subject><subject>DNA, Plant - genetics</subject><subject>Evolution, Molecular</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Life Sciences</subject><subject>Mathematical analysis</subject><subject>Mustard Plant - genetics</subject><subject>Plant Sciences</subject><issn>2055-0278</issn><issn>2055-0278</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp1kU1LxDAQhoMoKro_wIsUvHip5qNp0oug4hcIXvYe0nTajXQTTVph_fVmrd_gaSYzz7yZ4UXogOATgpk8jQUphMgxxTkWjOerDbRLMeepIuTmj3wHzWJ8xBgTwTkr8TbaYalMCyx3kTvPFrZb5Ma7wXajHVbZRdAxWqMzZ7ugsw6cX0LWe6N7-wox02awL5AZcENInbAuuSZroLUu5cMC0ttAHILuv8UmmX201eo-wuwj7qH59dX88ja_f7i5uzy_z00h8JAXRtSNbOumMsRUwAg2TUmpKCVoTuuykoTKFKA12JDSUF3XHIsCmOSkatkeOptkn8Z6Cc37qrpXT8EudVgpr6363XF2oTr_okRBKspIEjj-EAj-eUy3qKWNBvpeO_BjVLRgjDIppUjo0R_00Y_BpevWFC0lZ5ImikyUCT7GAO3XMgSrtZ9q8lMlP9XaT7VKM4c_r_ia-HQvAXQCYmq5DsL31_-rvgGhcK3J</recordid><startdate>20200801</startdate><enddate>20200801</enddate><creator>Perumal, Sampath</creator><creator>Koh, Chu Shin</creator><creator>Jin, Lingling</creator><creator>Buchwaldt, Miles</creator><creator>Higgins, Erin E.</creator><creator>Zheng, Chunfang</creator><creator>Sankoff, David</creator><creator>Robinson, Stephen J.</creator><creator>Kagale, Sateesh</creator><creator>Navabi, Zahra-Katy</creator><creator>Tang, Lily</creator><creator>Horner, Kyla N.</creator><creator>He, Zhesi</creator><creator>Bancroft, Ian</creator><creator>Chalhoub, Boulos</creator><creator>Sharpe, Andrew G.</creator><creator>Parkin, Isobel A. 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P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome</atitle><jtitle>Nature plants</jtitle><stitle>Nat. Plants</stitle><addtitle>Nat Plants</addtitle><date>2020-08-01</date><risdate>2020</risdate><volume>6</volume><issue>8</issue><spage>929</spage><epage>941</epage><pages>929-941</pages><issn>2055-0278</issn><eissn>2055-0278</eissn><abstract>It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed
Brassica nigra
, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication
Brassica-
specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating
B. nigra
from its diploid relatives.
Two high-quality nanopore genome assemblies of
Brassica nigra
are reported, one of which has particularly high contiguity with a contig N50 of 17.1 Mb, allowing localization of active centromeres and reconstruction of the ancestral
Brassica
genome.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>32782408</pmid><doi>10.1038/s41477-020-0735-y</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-8415-5189</orcidid><orcidid>https://orcid.org/0000-0001-8335-9876</orcidid><orcidid>https://orcid.org/0000-0001-7707-1171</orcidid><orcidid>https://orcid.org/0000-0002-1832-4009</orcidid><orcidid>https://orcid.org/0000-0002-7213-1590</orcidid><orcidid>https://orcid.org/0000-0002-5807-9466</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 45 45/23 45/91 631/208/2491 631/208/514/2254 Assemblies Biomedical and Life Sciences Brassica Brassica - genetics Brassica nigra Centromere - genetics Complexity Diploids DNA, Plant - genetics Evolution, Molecular Genome, Plant - genetics Genomes High-Throughput Nucleotide Sequencing Life Sciences Mathematical analysis Mustard Plant - genetics Plant Sciences |
| title | A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome |
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