Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume
NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. , an excellent horticultural cr...
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| Veröffentlicht in: | Genes 2018-10, Vol.9 (10), p.494 |
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| creator | Zhuo, Xiaokang Zheng, Tangchun Zhang, Zhiyong Zhang, Yichi Jiang, Liangbao Ahmad, Sagheer Sun, Lidan Wang, Jia Cheng, Tangren Zhang, Qixiang |
| description | NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity.
, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence
genes and characterized them by bioinformatics tools and expression profiles. These
s were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of
s were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (
/
/
) and three miRNA-targeted genes (
/
/
) were identified. Most
genes presented tissue-specific and time-specific expression patterns. Sixteen
s (
/
/
/
/
/
/
/
/
/
/
/
) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative
s was observed under 4 °C at different treatment times. The expression of 10 genes (
/
/
/
/
/
/
/
/
) was upregulated, while 5 genes (
/
/
/
/
) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the
gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants. |
| doi_str_mv | 10.3390/genes9100494 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6209978</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2120750760</sourcerecordid><originalsourceid>FETCH-LOGICAL-c412t-1088a6ef92ae66e8169711380b673850704d046e16d4deb5811e025e4273b703</originalsourceid><addsrcrecordid>eNpdUctq3EAQFCEhNo5vOYeBXHKInJ6HXpfAsn6CiZdkwUcxK7XsMdKMMj0y2d_Jl2bkFxvPZRq6qqurK0k-cjiSsoJvN2iRKg6gKvUm2RdQyFQpkb3dqfeSQ6I7iE-BAMjeJ3sSpBBQFvvJ3zO0bsD02rTIFlb3WzLEXMfCLbIfiyVbe22p8WYMxll2qpvgPIskjPVg-i37ifeoe2LHpuvQow1G9-zkz-iRaKasdAjoLTFtW7Z0fZv-CnMvEml0lpCYsQ9y1861W7bqtQ1s5Sc7ERumAT8k77oogIdP_0GyPj1ZL8_Ty6uzi-XiMm0UFyHlUJY6x64SGvMcS55XBeeyhE1eyDKDAlQLKkeet6rFTVZyjiAyVKKQmwLkQfL9cew4bQZsm-jE674evRm039ZOm_r_jjW39Y27r3MBVVWUccCXpwHe_Z6QQj0YarCPftBNVAseI4l75LPW51fQOzf5eP0HVMYzpdSM-vqIarwj8ti9LMOhnuOvd-OP8E-7Bl7Az2HLf4vmrKw</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2125154440</pqid></control><display><type>article</type><title>Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>PubMed Central Open Access</source><creator>Zhuo, Xiaokang ; Zheng, Tangchun ; Zhang, Zhiyong ; Zhang, Yichi ; Jiang, Liangbao ; Ahmad, Sagheer ; Sun, Lidan ; Wang, Jia ; Cheng, Tangren ; Zhang, Qixiang</creator><creatorcontrib>Zhuo, Xiaokang ; Zheng, Tangchun ; Zhang, Zhiyong ; Zhang, Yichi ; Jiang, Liangbao ; Ahmad, Sagheer ; Sun, Lidan ; Wang, Jia ; Cheng, Tangren ; Zhang, Qixiang</creatorcontrib><description>NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity.
, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence
genes and characterized them by bioinformatics tools and expression profiles. These
s were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of
s were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (
/
/
) and three miRNA-targeted genes (
/
/
) were identified. Most
genes presented tissue-specific and time-specific expression patterns. Sixteen
s (
/
/
/
/
/
/
/
/
/
/
/
) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative
s was observed under 4 °C at different treatment times. The expression of 10 genes (
/
/
/
/
/
/
/
/
) was upregulated, while 5 genes (
/
/
/
/
) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the
gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes9100494</identifier><identifier>PMID: 30322087</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Abiotic stress ; Abscisic acid ; Adaptation ; Apoptosis ; Bioinformatics ; Cell division ; Cellular stress response ; Chromosome 3 ; Cold ; Cold tolerance ; Deoxyribonucleic acid ; DNA ; Dormancy ; Engineering research ; Freezing ; Gene expression ; Genomes ; Laboratories ; Landscape architecture ; Melatonin ; Metabolism ; Metabolites ; MicroRNAs ; miRNA ; Plant breeding ; Polyamines ; Proteins ; Prunus mume ; Signal transduction ; Transcription factors ; Transduction ; Trends</subject><ispartof>Genes, 2018-10, Vol.9 (10), p.494</ispartof><rights>2018. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 by the authors. 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-1088a6ef92ae66e8169711380b673850704d046e16d4deb5811e025e4273b703</citedby><cites>FETCH-LOGICAL-c412t-1088a6ef92ae66e8169711380b673850704d046e16d4deb5811e025e4273b703</cites><orcidid>0000-0001-8612-7659 ; 0000-0003-2218-8350</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209978/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209978/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30322087$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhuo, Xiaokang</creatorcontrib><creatorcontrib>Zheng, Tangchun</creatorcontrib><creatorcontrib>Zhang, Zhiyong</creatorcontrib><creatorcontrib>Zhang, Yichi</creatorcontrib><creatorcontrib>Jiang, Liangbao</creatorcontrib><creatorcontrib>Ahmad, Sagheer</creatorcontrib><creatorcontrib>Sun, Lidan</creatorcontrib><creatorcontrib>Wang, Jia</creatorcontrib><creatorcontrib>Cheng, Tangren</creatorcontrib><creatorcontrib>Zhang, Qixiang</creatorcontrib><title>Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity.
, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence
genes and characterized them by bioinformatics tools and expression profiles. These
s were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of
s were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (
/
/
) and three miRNA-targeted genes (
/
/
) were identified. Most
genes presented tissue-specific and time-specific expression patterns. Sixteen
s (
/
/
/
/
/
/
/
/
/
/
/
) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative
s was observed under 4 °C at different treatment times. The expression of 10 genes (
/
/
/
/
/
/
/
/
) was upregulated, while 5 genes (
/
/
/
/
) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the
gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.</description><subject>Abiotic stress</subject><subject>Abscisic acid</subject><subject>Adaptation</subject><subject>Apoptosis</subject><subject>Bioinformatics</subject><subject>Cell division</subject><subject>Cellular stress response</subject><subject>Chromosome 3</subject><subject>Cold</subject><subject>Cold tolerance</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Dormancy</subject><subject>Engineering research</subject><subject>Freezing</subject><subject>Gene expression</subject><subject>Genomes</subject><subject>Laboratories</subject><subject>Landscape architecture</subject><subject>Melatonin</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>MicroRNAs</subject><subject>miRNA</subject><subject>Plant breeding</subject><subject>Polyamines</subject><subject>Proteins</subject><subject>Prunus mume</subject><subject>Signal transduction</subject><subject>Transcription factors</subject><subject>Transduction</subject><subject>Trends</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNpdUctq3EAQFCEhNo5vOYeBXHKInJ6HXpfAsn6CiZdkwUcxK7XsMdKMMj0y2d_Jl2bkFxvPZRq6qqurK0k-cjiSsoJvN2iRKg6gKvUm2RdQyFQpkb3dqfeSQ6I7iE-BAMjeJ3sSpBBQFvvJ3zO0bsD02rTIFlb3WzLEXMfCLbIfiyVbe22p8WYMxll2qpvgPIskjPVg-i37ifeoe2LHpuvQow1G9-zkz-iRaKasdAjoLTFtW7Z0fZv-CnMvEml0lpCYsQ9y1861W7bqtQ1s5Sc7ERumAT8k77oogIdP_0GyPj1ZL8_Ty6uzi-XiMm0UFyHlUJY6x64SGvMcS55XBeeyhE1eyDKDAlQLKkeet6rFTVZyjiAyVKKQmwLkQfL9cew4bQZsm-jE674evRm039ZOm_r_jjW39Y27r3MBVVWUccCXpwHe_Z6QQj0YarCPftBNVAseI4l75LPW51fQOzf5eP0HVMYzpdSM-vqIarwj8ti9LMOhnuOvd-OP8E-7Bl7Az2HLf4vmrKw</recordid><startdate>20181012</startdate><enddate>20181012</enddate><creator>Zhuo, Xiaokang</creator><creator>Zheng, Tangchun</creator><creator>Zhang, Zhiyong</creator><creator>Zhang, Yichi</creator><creator>Jiang, Liangbao</creator><creator>Ahmad, Sagheer</creator><creator>Sun, Lidan</creator><creator>Wang, Jia</creator><creator>Cheng, Tangren</creator><creator>Zhang, Qixiang</creator><general>MDPI AG</general><general>MDPI</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</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><orcidid>https://orcid.org/0000-0001-8612-7659</orcidid><orcidid>https://orcid.org/0000-0003-2218-8350</orcidid></search><sort><creationdate>20181012</creationdate><title>Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume</title><author>Zhuo, Xiaokang ; Zheng, Tangchun ; Zhang, Zhiyong ; Zhang, Yichi ; Jiang, Liangbao ; Ahmad, Sagheer ; Sun, Lidan ; Wang, Jia ; Cheng, Tangren ; Zhang, Qixiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-1088a6ef92ae66e8169711380b673850704d046e16d4deb5811e025e4273b703</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Abiotic stress</topic><topic>Abscisic acid</topic><topic>Adaptation</topic><topic>Apoptosis</topic><topic>Bioinformatics</topic><topic>Cell division</topic><topic>Cellular stress response</topic><topic>Chromosome 3</topic><topic>Cold</topic><topic>Cold tolerance</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Dormancy</topic><topic>Engineering research</topic><topic>Freezing</topic><topic>Gene expression</topic><topic>Genomes</topic><topic>Laboratories</topic><topic>Landscape architecture</topic><topic>Melatonin</topic><topic>Metabolism</topic><topic>Metabolites</topic><topic>MicroRNAs</topic><topic>miRNA</topic><topic>Plant breeding</topic><topic>Polyamines</topic><topic>Proteins</topic><topic>Prunus mume</topic><topic>Signal transduction</topic><topic>Transcription factors</topic><topic>Transduction</topic><topic>Trends</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhuo, Xiaokang</creatorcontrib><creatorcontrib>Zheng, Tangchun</creatorcontrib><creatorcontrib>Zhang, Zhiyong</creatorcontrib><creatorcontrib>Zhang, Yichi</creatorcontrib><creatorcontrib>Jiang, Liangbao</creatorcontrib><creatorcontrib>Ahmad, Sagheer</creatorcontrib><creatorcontrib>Sun, Lidan</creatorcontrib><creatorcontrib>Wang, Jia</creatorcontrib><creatorcontrib>Cheng, Tangren</creatorcontrib><creatorcontrib>Zhang, Qixiang</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhuo, Xiaokang</au><au>Zheng, Tangchun</au><au>Zhang, Zhiyong</au><au>Zhang, Yichi</au><au>Jiang, Liangbao</au><au>Ahmad, Sagheer</au><au>Sun, Lidan</au><au>Wang, Jia</au><au>Cheng, Tangren</au><au>Zhang, Qixiang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2018-10-12</date><risdate>2018</risdate><volume>9</volume><issue>10</issue><spage>494</spage><pages>494-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity.
, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence
genes and characterized them by bioinformatics tools and expression profiles. These
s were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of
s were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (
/
/
) and three miRNA-targeted genes (
/
/
) were identified. Most
genes presented tissue-specific and time-specific expression patterns. Sixteen
s (
/
/
/
/
/
/
/
/
/
/
/
) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
/
) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative
s was observed under 4 °C at different treatment times. The expression of 10 genes (
/
/
/
/
/
/
/
/
) was upregulated, while 5 genes (
/
/
/
/
) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the
gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>30322087</pmid><doi>10.3390/genes9100494</doi><orcidid>https://orcid.org/0000-0001-8612-7659</orcidid><orcidid>https://orcid.org/0000-0003-2218-8350</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Genes, 2018-10, Vol.9 (10), p.494 |
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| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6209978 |
| source | MDPI - Multidisciplinary Digital Publishing Institute; EZB-FREE-00999 freely available EZB journals; PubMed Central; PubMed Central Open Access |
| subjects | Abiotic stress Abscisic acid Adaptation Apoptosis Bioinformatics Cell division Cellular stress response Chromosome 3 Cold Cold tolerance Deoxyribonucleic acid DNA Dormancy Engineering research Freezing Gene expression Genomes Laboratories Landscape architecture Melatonin Metabolism Metabolites MicroRNAs miRNA Plant breeding Polyamines Proteins Prunus mume Signal transduction Transcription factors Transduction Trends |
| title | Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume |
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