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The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry gen...
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Published in: | DNA research 2017-10, Vol.24 (5), p.499-508 |
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creator | Shirasawa, Kenta Isuzugawa, Kanji Ikenaga, Mitsunobu Saito, Yutaro Yamamoto, Toshiya Hirakawa, Hideki Isobe, Sachiko |
description | We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)). |
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The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).</description><identifier>ISSN: 1340-2838</identifier><identifier>EISSN: 1756-1663</identifier><identifier>DOI: 10.1093/dnares/dsx020</identifier><identifier>PMID: 28541388</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Breeding - methods ; Genetic Variation ; Genome, Plant ; Genomics ; INDEL Mutation ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Prunus avium - genetics ; Prunus persica - genetics ; Sequence Analysis, DNA</subject><ispartof>DNA research, 2017-10, Vol.24 (5), p.499-508</ispartof><rights>The Author 2017. 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The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).</description><subject>Breeding - methods</subject><subject>Genetic Variation</subject><subject>Genome, Plant</subject><subject>Genomics</subject><subject>INDEL Mutation</subject><subject>Microsatellite Repeats</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Prunus avium - genetics</subject><subject>Prunus persica - genetics</subject><subject>Sequence Analysis, DNA</subject><issn>1340-2838</issn><issn>1756-1663</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNpVkU1P3DAQhq0KVGDbY6-Vj_SQ4q_YzqUSWtGChAQHkLhZsT3ZdbVxqCeB8u9JFYrgNCPNM-98vIR84ew7Z408ibktgCcR_zLBPpBDbmpdca3l3pxLxSphpT0gR4i_GVO8luYjORC2Vlxae0jubrZAN5CHHijCnwlyADp0FB8BRhq2UMoTPb4uU56Qtg9p6r_Rbih0QqApL50pYNUiJhwhUl8AYsqbT2S_a3cIn1_iitz-PLtZn1eXV78u1qeXVVCSj1VgUhhTq0Yr5o1lphOGm05qHZkXjdYmKi95tJrrxseGBx80Ex6Un7POyhX5sejeT76HGCCPpd25-5L6tjy5oU3ufSWnrdsMD6420kjdzALHLwJlmO_H0fUJA-x2bYZhQscbJpQVYuZXpFrQUAbEAt3rGM7cPzfc4oZb3Jj5r293e6X_v18-A4DPiS0</recordid><startdate>20171001</startdate><enddate>20171001</enddate><creator>Shirasawa, Kenta</creator><creator>Isuzugawa, Kanji</creator><creator>Ikenaga, Mitsunobu</creator><creator>Saito, Yutaro</creator><creator>Yamamoto, Toshiya</creator><creator>Hirakawa, Hideki</creator><creator>Isobe, Sachiko</creator><general>Oxford University Press</general><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>20171001</creationdate><title>The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding</title><author>Shirasawa, Kenta ; Isuzugawa, Kanji ; Ikenaga, Mitsunobu ; Saito, Yutaro ; Yamamoto, Toshiya ; Hirakawa, Hideki ; Isobe, Sachiko</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c431t-c03277549640b7807f2717f366d0b29667d4b31d86169bd91cbc602be4bcbcf83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Breeding - methods</topic><topic>Genetic Variation</topic><topic>Genome, Plant</topic><topic>Genomics</topic><topic>INDEL Mutation</topic><topic>Microsatellite Repeats</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Prunus avium - genetics</topic><topic>Prunus persica - genetics</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shirasawa, Kenta</creatorcontrib><creatorcontrib>Isuzugawa, Kanji</creatorcontrib><creatorcontrib>Ikenaga, Mitsunobu</creatorcontrib><creatorcontrib>Saito, Yutaro</creatorcontrib><creatorcontrib>Yamamoto, Toshiya</creatorcontrib><creatorcontrib>Hirakawa, Hideki</creatorcontrib><creatorcontrib>Isobe, Sachiko</creatorcontrib><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>DNA research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shirasawa, Kenta</au><au>Isuzugawa, Kanji</au><au>Ikenaga, Mitsunobu</au><au>Saito, Yutaro</au><au>Yamamoto, Toshiya</au><au>Hirakawa, Hideki</au><au>Isobe, Sachiko</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding</atitle><jtitle>DNA research</jtitle><addtitle>DNA Res</addtitle><date>2017-10-01</date><risdate>2017</risdate><volume>24</volume><issue>5</issue><spage>499</spage><epage>508</epage><pages>499-508</pages><issn>1340-2838</issn><eissn>1756-1663</eissn><abstract>We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>28541388</pmid><doi>10.1093/dnares/dsx020</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Breeding - methods Genetic Variation Genome, Plant Genomics INDEL Mutation Microsatellite Repeats Polymorphism, Single Nucleotide Prunus avium - genetics Prunus persica - genetics Sequence Analysis, DNA |
title | The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding |
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