De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome
The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular org...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/695947 |
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| author | Vladimir A. Zhukov Alexander I. Zhernakov Olga A. Kulaeva Nikita I. Ershov Alexey Y. Borisov Igor A. Tikhonovich |
| author_facet | Vladimir A. Zhukov Alexander I. Zhernakov Olga A. Kulaeva Nikita I. Ershov Alexey Y. Borisov Igor A. Tikhonovich |
| author_sort | Vladimir A. Zhukov |
| collection | DOAJ |
| description | The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR. |
| format | Article |
| id | doaj-art-00d1787131dd4f01a6e0b914d7ea46ff |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-00d1787131dd4f01a6e0b914d7ea46ff2025-02-03T06:07:04ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/695947695947De Novo Assembly of the Pea (Pisum sativum L.) Nodule TranscriptomeVladimir A. Zhukov0Alexander I. Zhernakov1Olga A. Kulaeva2Nikita I. Ershov3Alexey Y. Borisov4Igor A. Tikhonovich5All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, RussiaInstitute of Cytology & Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, RussiaAll-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Chausse 3, Saint Petersburg 196608, RussiaThe large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.http://dx.doi.org/10.1155/2015/695947 |
| spellingShingle | Vladimir A. Zhukov Alexander I. Zhernakov Olga A. Kulaeva Nikita I. Ershov Alexey Y. Borisov Igor A. Tikhonovich De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome International Journal of Genomics |
| title | De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome |
| title_full | De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome |
| title_fullStr | De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome |
| title_full_unstemmed | De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome |
| title_short | De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome |
| title_sort | de novo assembly of the pea pisum sativum l nodule transcriptome |
| url | http://dx.doi.org/10.1155/2015/695947 |
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