Dataset Information

SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer.

ABSTRACT: : SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts' genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers' cultivars farmers' cultivars of 4 years old ginsengs' roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What's more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts' expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age's molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts' biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

SUBMITTER: Li S

PROVIDER: S-EPMC7154844 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer.

Li Shaokun S Li Li L Jiang Yang Y Wu Jun J Sun Honghua H Zhao Mingzhu M Jiang Yue Y Zhu Lei L Wang Yanfang Y Su Yingjie Y Wang Kangyu K Wang Yi Y Zhang Meiping M

Plants (Basel, Switzerland) 20200311 3

: SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identificatio ...[more]

PMID: 32168804

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Project description:We aimed to investigate the effects of genome, age, and soil factors on cultivated Panax ginseng C. A. Meyer (CPG) compounds under identical climate and agronomic practices. Eight populations of CPG from different years and rhizosphere soils were collected from garden and cropland in the city of Ji'an, China. Inter-simple sequence repeat (ISSR) primers were used to detect genetic diversity and identity, and soil microbial community diversity. Soil enzyme activities and nutrients were also measured. The contents of total ginsenosides (TG), Rg1, Re, Rf, Rd, and ginsenoside extractions of CPG were analyzed by spectrophotometry and HPLC. The relative importance of each factor was analyzed by mathematical methods such as correlation analysis, stepwise line regression, and path analysis. Regression equations of similarity values of HPLC fingerprint (SVHF), richness index of HPLC fingerprint (RIHF) and the TG, Rg1, Re, Rf, and Rd contents with their respective significant correlation factors were obtained. For SVHF, the relative importance is age>microbial community diversity>genetic diversity. For RIHF, the relative importance is age>genetic diversity>microbial community diversity. For TG, Rg1, and Rf contents, the relative importance is age>microbial community diversity. Ginseng age and genetic identity influenced Rd content, and age was more important. Total phosphorus was the only directly negative effect on Re. According to regression equations and path analysis, increasing age and decreasing Shannon (H') could improve the TG, Rg1, and Rf contents, with little effect on SVHF. Adding age, genetic diversity, and decreasing Shannon (H') increased RIHF. Adding age and genetic identity could also improve Rd content. Appropriate decreases in total phosphorus might increase Re content. These findings are significant for CPG scientific cultivation methods, through which CPG bioactive ingredients could be finely controlled via regulation of genotypes and cultural conditions.

Project description:BACKGROUND: Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. RESULTS: Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. CONCLUSIONS: This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel unigenes identified here enlarge the available P. ginseng gene pool and will facilitate gene discovery. In addition, the identification of microRNAs and the prediction of targets from this study will provide information on gene transcriptional regulation in P. ginseng. Finally, the analysis of simple sequence repeats will provide genetic makers for molecular breeding and genetic applications in this species.

Dataset Information

SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer.

Publications

SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer.

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