Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process
Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcr...
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| Veröffentlicht in: | BMC genomics 2016-11, Vol.17 (1), p.935-935, Article 935 |
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| creator | Qiu, Lingling Jiang, Bo Fang, Jia Shen, Yike Fang, Zhongxiang Rm, Saravana Kumar Yi, Keke Shen, Chenjia Yan, Daoliang Zheng, Bingsong |
| description | Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory.
In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.
Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants. |
| doi_str_mv | 10.1186/s12864-016-3182-4 |
| format | Article |
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In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.
Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-016-3182-4</identifier><identifier>PMID: 27855649</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Carya - genetics ; Carya - metabolism ; Cellular signal transduction ; Computational Biology - methods ; Cytokinins - metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genetic aspects ; Genetic transcription ; Grafting ; Growth ; Hickories ; High-Throughput Nucleotide Sequencing ; Indoleacetic Acids - metabolism ; Molecular Sequence Annotation ; Physiological aspects ; Plant Growth Regulators - metabolism ; Protein Interaction Mapping ; Protein Interaction Maps ; Reproducibility of Results ; Signal Transduction ; Transcriptome</subject><ispartof>BMC genomics, 2016-11, Vol.17 (1), p.935-935, Article 935</ispartof><rights>COPYRIGHT 2016 BioMed Central Ltd.</rights><rights>Copyright BioMed Central 2016</rights><rights>The Author(s). 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-919494de449ae048512e03d004b1e3ffb55ce78387a5a858e0fbb5a8dc6a47143</citedby><cites>FETCH-LOGICAL-c528t-919494de449ae048512e03d004b1e3ffb55ce78387a5a858e0fbb5a8dc6a47143</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/PMC5114764/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114764/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27855649$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Qiu, Lingling</creatorcontrib><creatorcontrib>Jiang, Bo</creatorcontrib><creatorcontrib>Fang, Jia</creatorcontrib><creatorcontrib>Shen, Yike</creatorcontrib><creatorcontrib>Fang, Zhongxiang</creatorcontrib><creatorcontrib>Rm, Saravana Kumar</creatorcontrib><creatorcontrib>Yi, Keke</creatorcontrib><creatorcontrib>Shen, Chenjia</creatorcontrib><creatorcontrib>Yan, Daoliang</creatorcontrib><creatorcontrib>Zheng, Bingsong</creatorcontrib><title>Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory.
In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.
Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.</description><subject>Carya - genetics</subject><subject>Carya - metabolism</subject><subject>Cellular signal transduction</subject><subject>Computational Biology - methods</subject><subject>Cytokinins - metabolism</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene Ontology</subject><subject>Genetic aspects</subject><subject>Genetic transcription</subject><subject>Grafting</subject><subject>Growth</subject><subject>Hickories</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Indoleacetic Acids - metabolism</subject><subject>Molecular Sequence Annotation</subject><subject>Physiological aspects</subject><subject>Plant Growth Regulators - metabolism</subject><subject>Protein Interaction Mapping</subject><subject>Protein Interaction Maps</subject><subject>Reproducibility of Results</subject><subject>Signal Transduction</subject><subject>Transcriptome</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNptks1u1DAUhSMEoqXwAGyQJTatRIrt2LGzQRqN-KlUCYmfteU4N4lLYg92Usgj8NY4nVI6CHnha_u7x7pHJ8ueE3xOiCxfR0JlyXJMyrwgkubsQXZMmCA5JSV7eK8-yp7EeIUxEZLyx9kRFZLzklXH2a-N08MSbUS-RVPQLppgd5MfAVmHemu--bCg060Oi0ZGT71ewCX87BXSrkGzM_4aApp6QM3i9GhNXBvXc-_D6JM6irZLm3Ud2iWBH3pBzRzWYxd0O6Fd8AZifJo9avUQ4dntfpJ9fff2y_ZDfvnx_cV2c5kbTuWUV6RiFWuAsUoDZpITCrhoMGY1gaJta84NCFlIobmWXAJu6zpVjSl1soMVJ9mbve5urkdoDLg09qB2wY5pSOW1VYcvzvaq89eKk-RnuQqc3goE_32GOKnRRgPDoB34OSoiGRGVoIIn9OU_6JWfQzLjhuK0YiXHf6lOD6Csa33616yiasMEZawUN9T5f6i0GkiuewetTfcHDWcHDYmZ4OfU6TlGdfH50yFL9qwJPsYA7Z0fBKs1a2qfNZWyptasqdWHF_eNvOv4E67iN9ocz8Q</recordid><startdate>20161117</startdate><enddate>20161117</enddate><creator>Qiu, Lingling</creator><creator>Jiang, Bo</creator><creator>Fang, Jia</creator><creator>Shen, Yike</creator><creator>Fang, Zhongxiang</creator><creator>Rm, Saravana Kumar</creator><creator>Yi, Keke</creator><creator>Shen, Chenjia</creator><creator>Yan, Daoliang</creator><creator>Zheng, Bingsong</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161117</creationdate><title>Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process</title><author>Qiu, Lingling ; Jiang, Bo ; Fang, Jia ; Shen, Yike ; Fang, Zhongxiang ; Rm, Saravana Kumar ; Yi, Keke ; Shen, Chenjia ; Yan, Daoliang ; Zheng, Bingsong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-919494de449ae048512e03d004b1e3ffb55ce78387a5a858e0fbb5a8dc6a47143</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Carya - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qiu, Lingling</au><au>Jiang, Bo</au><au>Fang, Jia</au><au>Shen, Yike</au><au>Fang, Zhongxiang</au><au>Rm, Saravana Kumar</au><au>Yi, Keke</au><au>Shen, Chenjia</au><au>Yan, Daoliang</au><au>Zheng, Bingsong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2016-11-17</date><risdate>2016</risdate><volume>17</volume><issue>1</issue><spage>935</spage><epage>935</epage><pages>935-935</pages><artnum>935</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory.
In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.
Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>27855649</pmid><doi>10.1186/s12864-016-3182-4</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Carya - genetics Carya - metabolism Cellular signal transduction Computational Biology - methods Cytokinins - metabolism Gene Expression Profiling Gene Expression Regulation, Plant Gene Ontology Genetic aspects Genetic transcription Grafting Growth Hickories High-Throughput Nucleotide Sequencing Indoleacetic Acids - metabolism Molecular Sequence Annotation Physiological aspects Plant Growth Regulators - metabolism Protein Interaction Mapping Protein Interaction Maps Reproducibility of Results Signal Transduction Transcriptome |
| title | Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process |
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