{"title":"西瓜（Citrullus lanatus）果实发育过程中 SSR2 基因的全基因组鉴定和表达分析","authors":"Jing Zhang, Yan-Ge Li, Hao-Ting Sun, Ding-Ding Zuo, Yang Qiao, Rui Sun, Jia-Lin Xing, Zhong-Hou Zhu, Xue-Jie Zhu, Da-Long Guo","doi":"10.1186/s40538-024-00624-7","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p>Sterol side-chain reductase 2 (SSR2) is a key enzyme in the synthesis of plant cholesterol pathway. Despite the importance of watermelon as a horticultural cash crop, the SSR2 gene in watermelon has not been previously studied or reported.</p><h3>Results</h3><p>In this study, 28 SSR2 genes were identified in the watermelon genome. The physicochemical properties of 28 <i>ClaSSR</i> proteins were predicted by bioinformatics methods, and the gene structure, conserved motif, chromosome localization, phylogenetic analysis, cis-acting elements, expression patterns, promoter activity analysis and subcellular localization of <i>ClaSSRs</i> were studied. The 28 <i>ClaSSRs</i> were unevenly distributed on 11 chromosomes, and phylogenetic analysis showed that they could be grouped into 4 groups with other related Cucurbitaceae homologous genes. Analysis of gene structure and motifs revealed similarities in exons/introns and motifs between members of the same group, further supporting phylogenetic results. The RT–qPCR results showed variations in <i>ClaSSRs</i> expression during watermelon fruit development. The analysis of promoter activity for <i>ClaSSR25</i> showed strong activity. Subcellular localization studies confirmed that <i>ClaSSR25</i> is mainly located in the cytoplasm, which aligns with the predicted outcomes. We additionally estimated the network of protein–protein interactions for <i>ClaSSR25</i> and analyzed proteins that could potentially interact with <i>ClaSSR25</i> in melon and <i>Arabidopsis thaliana</i>.</p><h3>Conclusions</h3><p>We conducted bioinformatics analysis and expression analysis of members of the watermelon SSR2 gene family in this work, and the outcomes set the stage for further investigations into the watermelon SSR2 gene.</p><h3>Graphical Abstract</h3>\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":512,"journal":{"name":"Chemical and Biological Technologies in Agriculture","volume":"11 1","pages":""},"PeriodicalIF":5.2000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chembioagro.springeropen.com/counter/pdf/10.1186/s40538-024-00624-7","citationCount":"0","resultStr":"{\"title\":\"Genome-wide identification and expression analysis of watermelon (Citrullus lanatus) SSR2 gene during fruit development\",\"authors\":\"Jing Zhang, Yan-Ge Li, Hao-Ting Sun, Ding-Ding Zuo, Yang Qiao, Rui Sun, Jia-Lin Xing, Zhong-Hou Zhu, Xue-Jie Zhu, Da-Long Guo\",\"doi\":\"10.1186/s40538-024-00624-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p>Sterol side-chain reductase 2 (SSR2) is a key enzyme in the synthesis of plant cholesterol pathway. Despite the importance of watermelon as a horticultural cash crop, the SSR2 gene in watermelon has not been previously studied or reported.</p><h3>Results</h3><p>In this study, 28 SSR2 genes were identified in the watermelon genome. The physicochemical properties of 28 <i>ClaSSR</i> proteins were predicted by bioinformatics methods, and the gene structure, conserved motif, chromosome localization, phylogenetic analysis, cis-acting elements, expression patterns, promoter activity analysis and subcellular localization of <i>ClaSSRs</i> were studied. The 28 <i>ClaSSRs</i> were unevenly distributed on 11 chromosomes, and phylogenetic analysis showed that they could be grouped into 4 groups with other related Cucurbitaceae homologous genes. Analysis of gene structure and motifs revealed similarities in exons/introns and motifs between members of the same group, further supporting phylogenetic results. The RT–qPCR results showed variations in <i>ClaSSRs</i> expression during watermelon fruit development. The analysis of promoter activity for <i>ClaSSR25</i> showed strong activity. Subcellular localization studies confirmed that <i>ClaSSR25</i> is mainly located in the cytoplasm, which aligns with the predicted outcomes. We additionally estimated the network of protein–protein interactions for <i>ClaSSR25</i> and analyzed proteins that could potentially interact with <i>ClaSSR25</i> in melon and <i>Arabidopsis thaliana</i>.</p><h3>Conclusions</h3><p>We conducted bioinformatics analysis and expression analysis of members of the watermelon SSR2 gene family in this work, and the outcomes set the stage for further investigations into the watermelon SSR2 gene.</p><h3>Graphical Abstract</h3>\\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>\",\"PeriodicalId\":512,\"journal\":{\"name\":\"Chemical and Biological Technologies in Agriculture\",\"volume\":\"11 1\",\"pages\":\"\"},\"PeriodicalIF\":5.2000,\"publicationDate\":\"2024-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://chembioagro.springeropen.com/counter/pdf/10.1186/s40538-024-00624-7\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Chemical and Biological Technologies in Agriculture\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://link.springer.com/article/10.1186/s40538-024-00624-7\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chemical and Biological Technologies in Agriculture","FirstCategoryId":"97","ListUrlMain":"https://link.springer.com/article/10.1186/s40538-024-00624-7","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, MULTIDISCIPLINARY","Score":null,"Total":0}
Genome-wide identification and expression analysis of watermelon (Citrullus lanatus) SSR2 gene during fruit development
Background
Sterol side-chain reductase 2 (SSR2) is a key enzyme in the synthesis of plant cholesterol pathway. Despite the importance of watermelon as a horticultural cash crop, the SSR2 gene in watermelon has not been previously studied or reported.
Results
In this study, 28 SSR2 genes were identified in the watermelon genome. The physicochemical properties of 28 ClaSSR proteins were predicted by bioinformatics methods, and the gene structure, conserved motif, chromosome localization, phylogenetic analysis, cis-acting elements, expression patterns, promoter activity analysis and subcellular localization of ClaSSRs were studied. The 28 ClaSSRs were unevenly distributed on 11 chromosomes, and phylogenetic analysis showed that they could be grouped into 4 groups with other related Cucurbitaceae homologous genes. Analysis of gene structure and motifs revealed similarities in exons/introns and motifs between members of the same group, further supporting phylogenetic results. The RT–qPCR results showed variations in ClaSSRs expression during watermelon fruit development. The analysis of promoter activity for ClaSSR25 showed strong activity. Subcellular localization studies confirmed that ClaSSR25 is mainly located in the cytoplasm, which aligns with the predicted outcomes. We additionally estimated the network of protein–protein interactions for ClaSSR25 and analyzed proteins that could potentially interact with ClaSSR25 in melon and Arabidopsis thaliana.
Conclusions
We conducted bioinformatics analysis and expression analysis of members of the watermelon SSR2 gene family in this work, and the outcomes set the stage for further investigations into the watermelon SSR2 gene.
期刊介绍：
Chemical and Biological Technologies in Agriculture is an international, interdisciplinary, peer-reviewed forum for the advancement and application to all fields of agriculture of modern chemical, biochemical and molecular technologies. The scope of this journal includes chemical and biochemical processes aimed to increase sustainable agricultural and food production, the evaluation of quality and origin of raw primary products and their transformation into foods and chemicals, as well as environmental monitoring and remediation. Of special interest are the effects of chemical and biochemical technologies, also at the nano and supramolecular scale, on the relationships between soil, plants, microorganisms and their environment, with the help of modern bioinformatics. Another special focus is the use of modern bioorganic and biological chemistry to develop new technologies for plant nutrition and bio-stimulation, advancement of biorefineries from biomasses, safe and traceable food products, carbon storage in soil and plants and restoration of contaminated soils to agriculture.
This journal presents the first opportunity to bring together researchers from a wide number of disciplines within the agricultural chemical and biological sciences, from both industry and academia. The principle aim of Chemical and Biological Technologies in Agriculture is to allow the exchange of the most advanced chemical and biochemical knowledge to develop technologies which address one of the most pressing challenges of our times - sustaining a growing world population.
Chemical and Biological Technologies in Agriculture publishes original research articles, short letters and invited reviews. Articles from scientists in industry, academia as well as private research institutes, non-governmental and environmental organizations are encouraged.
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