The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome
Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean ( Vigna angularis ) genome using single molecule real-time (SMRT) s...
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| Veröffentlicht in: | Scientific reports 2015-11, Vol.5 (1), p.16780-16780, Article 16780 |
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| creator | Sakai, Hiroaki Naito, Ken Ogiso-Tanaka, Eri Takahashi, Yu Iseki, Kohtaro Muto, Chiaki Satou, Kazuhito Teruya, Kuniko Shiroma, Akino Shimoji, Makiko Hirano, Takashi Itoh, Takeshi Kaga, Akito Tomooka, Norihiko |
| description | Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (
Vigna angularis
) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome. |
| doi_str_mv | 10.1038/srep16780 |
| format | Article |
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Vigna angularis
) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep16780</identifier><identifier>PMID: 26616024</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/208/726 ; 631/449/2491 ; Chromosome Mapping ; Computational Biology - instrumentation ; Computational Biology - methods ; Eukaryota - genetics ; Fabaceae - genetics ; Genetic Linkage ; Genome ; Genome, Plant ; Genomics - instrumentation ; Genomics - methods ; High-Throughput Nucleotide Sequencing - instrumentation ; High-Throughput Nucleotide Sequencing - methods ; Humanities and Social Sciences ; Molecular Sequence Annotation ; multidisciplinary ; Reproducibility of Results ; Science</subject><ispartof>Scientific reports, 2015-11, Vol.5 (1), p.16780-16780, Article 16780</ispartof><rights>The Author(s) 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c476t-a4a06914b1fff1a1f3b51f8e13bdc8b74d0e33b846a58178394278994989aeda3</citedby><cites>FETCH-LOGICAL-c476t-a4a06914b1fff1a1f3b51f8e13bdc8b74d0e33b846a58178394278994989aeda3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663752/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663752/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26616024$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sakai, Hiroaki</creatorcontrib><creatorcontrib>Naito, Ken</creatorcontrib><creatorcontrib>Ogiso-Tanaka, Eri</creatorcontrib><creatorcontrib>Takahashi, Yu</creatorcontrib><creatorcontrib>Iseki, Kohtaro</creatorcontrib><creatorcontrib>Muto, Chiaki</creatorcontrib><creatorcontrib>Satou, Kazuhito</creatorcontrib><creatorcontrib>Teruya, Kuniko</creatorcontrib><creatorcontrib>Shiroma, Akino</creatorcontrib><creatorcontrib>Shimoji, Makiko</creatorcontrib><creatorcontrib>Hirano, Takashi</creatorcontrib><creatorcontrib>Itoh, Takeshi</creatorcontrib><creatorcontrib>Kaga, Akito</creatorcontrib><creatorcontrib>Tomooka, Norihiko</creatorcontrib><title>The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (
Vigna angularis
) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.</description><subject>631/208/726</subject><subject>631/449/2491</subject><subject>Chromosome Mapping</subject><subject>Computational Biology - instrumentation</subject><subject>Computational Biology - methods</subject><subject>Eukaryota - genetics</subject><subject>Fabaceae - genetics</subject><subject>Genetic Linkage</subject><subject>Genome</subject><subject>Genome, Plant</subject><subject>Genomics - instrumentation</subject><subject>Genomics - methods</subject><subject>High-Throughput Nucleotide Sequencing - instrumentation</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humanities and Social Sciences</subject><subject>Molecular Sequence Annotation</subject><subject>multidisciplinary</subject><subject>Reproducibility of Results</subject><subject>Science</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><recordid>eNptkU1LHTEUhkOpqFgX_gHJ0hamzddkko1QpH6A4EbXIZM5M3c0k1yTGeX--0auvVgwm3PgffLm5LwInVDykxKufuUEayobRb6gQ0ZEXTHO2NcP_QE6zvmRlFMzLajeRwdMSioJE4fo6X4FeB1fIeHY4zyGwQOeoge3lCaB9dU8ToAzPC8QXNHxDG4Voo_DBo8Bz-V-BzjEl4htzjC1fvNmZTEsTzZt4jw6PECIE3xDe731GY7f6xF6uPxzf3Fd3d5d3Vz8vq2caORcWWGJ1FS0tO97amnP25r2CihvO6faRnQEOG-VkLZWtFFcC9YorYVW2kJn-RE63_qul3aCzkGYk_VmncapDGSiHc3_ShhXZogvRkjJm5oVg7N3gxTLt_NspjE78N4GiEs2tOFKKMpqXdDvW9SlmEsU_e4ZSsxbPmaXT2FPP861I_-lUYAfWyAXKQyQzGNcUii7-sTtL9aKm9w</recordid><startdate>20151130</startdate><enddate>20151130</enddate><creator>Sakai, Hiroaki</creator><creator>Naito, Ken</creator><creator>Ogiso-Tanaka, Eri</creator><creator>Takahashi, Yu</creator><creator>Iseki, Kohtaro</creator><creator>Muto, Chiaki</creator><creator>Satou, Kazuhito</creator><creator>Teruya, Kuniko</creator><creator>Shiroma, Akino</creator><creator>Shimoji, Makiko</creator><creator>Hirano, Takashi</creator><creator>Itoh, Takeshi</creator><creator>Kaga, Akito</creator><creator>Tomooka, Norihiko</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20151130</creationdate><title>The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome</title><author>Sakai, Hiroaki ; Naito, Ken ; Ogiso-Tanaka, Eri ; Takahashi, Yu ; Iseki, Kohtaro ; Muto, Chiaki ; Satou, Kazuhito ; Teruya, Kuniko ; Shiroma, Akino ; Shimoji, Makiko ; Hirano, Takashi ; Itoh, Takeshi ; Kaga, Akito ; Tomooka, Norihiko</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c476t-a4a06914b1fff1a1f3b51f8e13bdc8b74d0e33b846a58178394278994989aeda3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/208/726</topic><topic>631/449/2491</topic><topic>Chromosome Mapping</topic><topic>Computational Biology - instrumentation</topic><topic>Computational Biology - methods</topic><topic>Eukaryota - genetics</topic><topic>Fabaceae - genetics</topic><topic>Genetic Linkage</topic><topic>Genome</topic><topic>Genome, Plant</topic><topic>Genomics - instrumentation</topic><topic>Genomics - methods</topic><topic>High-Throughput Nucleotide Sequencing - instrumentation</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humanities and Social Sciences</topic><topic>Molecular Sequence Annotation</topic><topic>multidisciplinary</topic><topic>Reproducibility of Results</topic><topic>Science</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sakai, Hiroaki</creatorcontrib><creatorcontrib>Naito, Ken</creatorcontrib><creatorcontrib>Ogiso-Tanaka, Eri</creatorcontrib><creatorcontrib>Takahashi, Yu</creatorcontrib><creatorcontrib>Iseki, Kohtaro</creatorcontrib><creatorcontrib>Muto, Chiaki</creatorcontrib><creatorcontrib>Satou, Kazuhito</creatorcontrib><creatorcontrib>Teruya, Kuniko</creatorcontrib><creatorcontrib>Shiroma, Akino</creatorcontrib><creatorcontrib>Shimoji, Makiko</creatorcontrib><creatorcontrib>Hirano, Takashi</creatorcontrib><creatorcontrib>Itoh, Takeshi</creatorcontrib><creatorcontrib>Kaga, Akito</creatorcontrib><creatorcontrib>Tomooka, Norihiko</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sakai, Hiroaki</au><au>Naito, Ken</au><au>Ogiso-Tanaka, Eri</au><au>Takahashi, Yu</au><au>Iseki, Kohtaro</au><au>Muto, Chiaki</au><au>Satou, Kazuhito</au><au>Teruya, Kuniko</au><au>Shiroma, Akino</au><au>Shimoji, Makiko</au><au>Hirano, Takashi</au><au>Itoh, Takeshi</au><au>Kaga, Akito</au><au>Tomooka, Norihiko</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-11-30</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>16780</spage><epage>16780</epage><pages>16780-16780</pages><artnum>16780</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (
Vigna angularis
) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26616024</pmid><doi>10.1038/srep16780</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/208/726 631/449/2491 Chromosome Mapping Computational Biology - instrumentation Computational Biology - methods Eukaryota - genetics Fabaceae - genetics Genetic Linkage Genome Genome, Plant Genomics - instrumentation Genomics - methods High-Throughput Nucleotide Sequencing - instrumentation High-Throughput Nucleotide Sequencing - methods Humanities and Social Sciences Molecular Sequence Annotation multidisciplinary Reproducibility of Results Science |
| title | The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome |
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