Genome-Wide Identification and Expression Analysis of the MADS-Box Family in Ginkgo biloba
As the most significant transformation stage of plants, the flowering process has typically been the focus of research. MADS-box gene plays an important regulatory role in flower development. In this study, 26 MADS-box genes were identified from Ginkgo biloba, including 10 type-I genes and 16 type-I...
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| Veröffentlicht in: | Forests 2022-11, Vol.13 (11), p.1953 |
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| creator | Yang, Ke Liu, Zhongbing Chen, Xueyin Zhou, Xian Ye, Jiabao Xu, Feng Zhang, Weiwei Liao, Yongling Yang, Xiaoyan Wang, Qijian |
| description | As the most significant transformation stage of plants, the flowering process has typically been the focus of research. MADS-box gene plays an important regulatory role in flower development. In this study, 26 MADS-box genes were identified from Ginkgo biloba, including 10 type-I genes and 16 type-II genes, which were distributed on eight chromosomes. There was no collinearity between the GbMADS genes, and the homology with genes from other species was low. All GbMADS proteins contain conserved MADS domains. The gene structures of GbMADS in the same gene family or subfamily differed, but the conserved protein motifs had similar distributions. The microRNA (miRNA) target sites of the GbMADS genes were predicted. It was found that the expression of 16 GbMADS genes may be regulated by miRNA. The results of cis-acting element analysis showed that the 26 GbMADS genes contained a large number of hormones regulated and light-responsive elements as well as stress-response elements. Furthermore, the quantitative real-time PCR (qRT-PCR) experimental results showed that most GbMADS genes were differentially expressed in the male and female flowers at different developmental stages. Among them, the only MIKC * gene GbMADS16 has the highest expression in the metaphase development of the microstrobilus (M2) stage and is almost not expressed in female flowers. Taken together, these findings suggest that the MADS-box genes may play an important role in the development and differentiation of G. biloba flowers. |
| doi_str_mv | 10.3390/f13111953 |
| format | Article |
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MADS-box gene plays an important regulatory role in flower development. In this study, 26 MADS-box genes were identified from Ginkgo biloba, including 10 type-I genes and 16 type-II genes, which were distributed on eight chromosomes. There was no collinearity between the GbMADS genes, and the homology with genes from other species was low. All GbMADS proteins contain conserved MADS domains. The gene structures of GbMADS in the same gene family or subfamily differed, but the conserved protein motifs had similar distributions. The microRNA (miRNA) target sites of the GbMADS genes were predicted. It was found that the expression of 16 GbMADS genes may be regulated by miRNA. The results of cis-acting element analysis showed that the 26 GbMADS genes contained a large number of hormones regulated and light-responsive elements as well as stress-response elements. Furthermore, the quantitative real-time PCR (qRT-PCR) experimental results showed that most GbMADS genes were differentially expressed in the male and female flowers at different developmental stages. Among them, the only MIKC * gene GbMADS16 has the highest expression in the metaphase development of the microstrobilus (M2) stage and is almost not expressed in female flowers. Taken together, these findings suggest that the MADS-box genes may play an important role in the development and differentiation of G. biloba flowers.</description><identifier>ISSN: 1999-4907</identifier><identifier>EISSN: 1999-4907</identifier><identifier>DOI: 10.3390/f13111953</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>Alzheimer's disease ; Chromosomes ; Collinearity ; Developmental stages ; Females ; Flowering ; Flowers ; Flowers & plants ; Gene expression ; Genes ; Genetic aspects ; Genetic transformation ; Genomes ; Ginkgo ; Ginkgo biloba ; Homology ; Hormones ; Identification and classification ; MADS box proteins ; Metaphase ; MicroRNA ; miRNA ; Phylogenetics ; Physiological aspects ; Plants (botany) ; Proteins ; Regulatory sequences ; Ribonucleic acid ; RNA ; Software ; Trees</subject><ispartof>Forests, 2022-11, Vol.13 (11), p.1953</ispartof><rights>COPYRIGHT 2022 MDPI AG</rights><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c331t-2094a0a05313f71f488a2615b40fdd50afd44355956abf5b825ad59efdf7de603</citedby><cites>FETCH-LOGICAL-c331t-2094a0a05313f71f488a2615b40fdd50afd44355956abf5b825ad59efdf7de603</cites><orcidid>0000-0003-3212-6284</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids></links><search><creatorcontrib>Yang, Ke</creatorcontrib><creatorcontrib>Liu, Zhongbing</creatorcontrib><creatorcontrib>Chen, Xueyin</creatorcontrib><creatorcontrib>Zhou, Xian</creatorcontrib><creatorcontrib>Ye, Jiabao</creatorcontrib><creatorcontrib>Xu, Feng</creatorcontrib><creatorcontrib>Zhang, Weiwei</creatorcontrib><creatorcontrib>Liao, Yongling</creatorcontrib><creatorcontrib>Yang, Xiaoyan</creatorcontrib><creatorcontrib>Wang, Qijian</creatorcontrib><title>Genome-Wide Identification and Expression Analysis of the MADS-Box Family in Ginkgo biloba</title><title>Forests</title><description>As the most significant transformation stage of plants, the flowering process has typically been the focus of research. MADS-box gene plays an important regulatory role in flower development. In this study, 26 MADS-box genes were identified from Ginkgo biloba, including 10 type-I genes and 16 type-II genes, which were distributed on eight chromosomes. There was no collinearity between the GbMADS genes, and the homology with genes from other species was low. All GbMADS proteins contain conserved MADS domains. The gene structures of GbMADS in the same gene family or subfamily differed, but the conserved protein motifs had similar distributions. The microRNA (miRNA) target sites of the GbMADS genes were predicted. It was found that the expression of 16 GbMADS genes may be regulated by miRNA. The results of cis-acting element analysis showed that the 26 GbMADS genes contained a large number of hormones regulated and light-responsive elements as well as stress-response elements. Furthermore, the quantitative real-time PCR (qRT-PCR) experimental results showed that most GbMADS genes were differentially expressed in the male and female flowers at different developmental stages. Among them, the only MIKC * gene GbMADS16 has the highest expression in the metaphase development of the microstrobilus (M2) stage and is almost not expressed in female flowers. Taken together, these findings suggest that the MADS-box genes may play an important role in the development and differentiation of G. biloba flowers.</description><subject>Alzheimer's disease</subject><subject>Chromosomes</subject><subject>Collinearity</subject><subject>Developmental stages</subject><subject>Females</subject><subject>Flowering</subject><subject>Flowers</subject><subject>Flowers & plants</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic transformation</subject><subject>Genomes</subject><subject>Ginkgo</subject><subject>Ginkgo biloba</subject><subject>Homology</subject><subject>Hormones</subject><subject>Identification and classification</subject><subject>MADS box proteins</subject><subject>Metaphase</subject><subject>MicroRNA</subject><subject>miRNA</subject><subject>Phylogenetics</subject><subject>Physiological aspects</subject><subject>Plants (botany)</subject><subject>Proteins</subject><subject>Regulatory sequences</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Software</subject><subject>Trees</subject><issn>1999-4907</issn><issn>1999-4907</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpNUM9LwzAYDaLgmDv4HwQ8eehMmqRpjnVudTDxoCJ4KWmTzMw2mUkH239vx0T83uH7wXuPjwfANUZTQgS6M5hgjAUjZ2CEhRAJFYif_5svwSTGDRqK8VykdAQ-Su18p5N3qzRcKu16a2wje-sdlE7B-X4bdIzHtXCyPUQboTew_9TwqXh4Se79Hi5kZ9sDtA6W1n2tPaxt62t5BS6MbKOe_PYxeFvMX2ePyeq5XM6KVdIQgvskRYJKJBEjmBiODc1zmWaY1RQZpRiSRlFKGBMsk7VhdZ4yqZjQRhmudIbIGNycfLfBf-907KuN34Xh2VilnOYp5xnjA2t6Yq1lqyvrjO-DbAYo3dnGO23scC84ZRzlnOSD4PYkaIKPMWhTbYPtZDhUGFXHuKu_uMkPVjxv3g</recordid><startdate>20221101</startdate><enddate>20221101</enddate><creator>Yang, Ke</creator><creator>Liu, Zhongbing</creator><creator>Chen, Xueyin</creator><creator>Zhou, Xian</creator><creator>Ye, Jiabao</creator><creator>Xu, Feng</creator><creator>Zhang, Weiwei</creator><creator>Liao, Yongling</creator><creator>Yang, Xiaoyan</creator><creator>Wang, Qijian</creator><general>MDPI AG</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>M0K</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PYCSY</scope><orcidid>https://orcid.org/0000-0003-3212-6284</orcidid></search><sort><creationdate>20221101</creationdate><title>Genome-Wide Identification and Expression Analysis of the MADS-Box Family in Ginkgo biloba</title><author>Yang, Ke ; 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MADS-box gene plays an important regulatory role in flower development. In this study, 26 MADS-box genes were identified from Ginkgo biloba, including 10 type-I genes and 16 type-II genes, which were distributed on eight chromosomes. There was no collinearity between the GbMADS genes, and the homology with genes from other species was low. All GbMADS proteins contain conserved MADS domains. The gene structures of GbMADS in the same gene family or subfamily differed, but the conserved protein motifs had similar distributions. The microRNA (miRNA) target sites of the GbMADS genes were predicted. It was found that the expression of 16 GbMADS genes may be regulated by miRNA. The results of cis-acting element analysis showed that the 26 GbMADS genes contained a large number of hormones regulated and light-responsive elements as well as stress-response elements. Furthermore, the quantitative real-time PCR (qRT-PCR) experimental results showed that most GbMADS genes were differentially expressed in the male and female flowers at different developmental stages. Among them, the only MIKC * gene GbMADS16 has the highest expression in the metaphase development of the microstrobilus (M2) stage and is almost not expressed in female flowers. Taken together, these findings suggest that the MADS-box genes may play an important role in the development and differentiation of G. biloba flowers.</abstract><cop>Basel</cop><pub>MDPI AG</pub><doi>10.3390/f13111953</doi><orcidid>https://orcid.org/0000-0003-3212-6284</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; MDPI - Multidisciplinary Digital Publishing Institute |
| subjects | Alzheimer's disease Chromosomes Collinearity Developmental stages Females Flowering Flowers Flowers & plants Gene expression Genes Genetic aspects Genetic transformation Genomes Ginkgo Ginkgo biloba Homology Hormones Identification and classification MADS box proteins Metaphase MicroRNA miRNA Phylogenetics Physiological aspects Plants (botany) Proteins Regulatory sequences Ribonucleic acid RNA Software Trees |
| title | Genome-Wide Identification and Expression Analysis of the MADS-Box Family in Ginkgo biloba |
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