Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology
<p>Abstract</p> <p>Background</p> <p>Carnation (<it>Dianthus caryophyllus</it> L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flo...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/292 |
| _version_ | 1818556442957840384 |
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| author | Tanase Koji Nishitani Chikako Hirakawa Hideki Isobe Sachiko Tabata Satoshi Ohmiya Akemi Onozaki Takashi |
| author_facet | Tanase Koji Nishitani Chikako Hirakawa Hideki Isobe Sachiko Tabata Satoshi Ohmiya Akemi Onozaki Takashi |
| author_sort | Tanase Koji |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Carnation (<it>Dianthus caryophyllus</it> L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology.</p> <p>Results</p> <p>We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an <it>Arabidopsis</it> sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway.</p> <p>Conclusions</p> <p>We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.</p> |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-12-13T23:47:25Z |
| publishDate | 2012-07-01 |
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| spelling | doaj.art-5f7adc709c79407987c188c9023da6cd2022-12-21T23:26:54ZengBMCBMC Genomics1471-21642012-07-0113129210.1186/1471-2164-13-292Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technologyTanase KojiNishitani ChikakoHirakawa HidekiIsobe SachikoTabata SatoshiOhmiya AkemiOnozaki Takashi<p>Abstract</p> <p>Background</p> <p>Carnation (<it>Dianthus caryophyllus</it> L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology.</p> <p>Results</p> <p>We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an <it>Arabidopsis</it> sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway.</p> <p>Conclusions</p> <p>We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.</p>http://www.biomedcentral.com/1471-2164/13/292Carnation<it>Dianthus caryopyllus</it> L<it>.</it>Next-generation sequencing technologySSRTranscriptome |
| spellingShingle | Tanase Koji Nishitani Chikako Hirakawa Hideki Isobe Sachiko Tabata Satoshi Ohmiya Akemi Onozaki Takashi Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology BMC Genomics Carnation <it>Dianthus caryopyllus</it> L<it>.</it> Next-generation sequencing technology SSR Transcriptome |
| title | Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology |
| title_full | Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology |
| title_fullStr | Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology |
| title_full_unstemmed | Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology |
| title_short | Transcriptome analysis of carnation (<it>Dianthus caryophyllus</it> L.) based on next-generation sequencing technology |
| title_sort | transcriptome analysis of carnation it dianthus caryophyllus it l based on next generation sequencing technology |
| topic | Carnation <it>Dianthus caryopyllus</it> L<it>.</it> Next-generation sequencing technology SSR Transcriptome |
| url | http://www.biomedcentral.com/1471-2164/13/292 |
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