Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors
Sugar, the primary product of photosynthesis, is a vital requirement for cell activities. Allocation of sugar from source to sink tissues is facilitated by sugar transporters (ST). These STs belong to the Major Facilitator Superfamily (MFS), the largest family of STs in plants. In this study, we per...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1502649/full |
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| author | Sehrish Akbar Xuiting Hua Yingying Zhang Gang Liu Tianyou Wang Huihong Shi Zhen Li Yiying Qi Habiba Habiba Wei Yao Mu-Qing Zhang Jisen Zhang |
| author_facet | Sehrish Akbar Xuiting Hua Yingying Zhang Gang Liu Tianyou Wang Huihong Shi Zhen Li Yiying Qi Habiba Habiba Wei Yao Mu-Qing Zhang Jisen Zhang |
| author_sort | Sehrish Akbar |
| collection | DOAJ |
| description | Sugar, the primary product of photosynthesis, is a vital requirement for cell activities. Allocation of sugar from source to sink tissues is facilitated by sugar transporters (ST). These STs belong to the Major Facilitator Superfamily (MFS), the largest family of STs in plants. In this study, we performed genome wide and gene expression data analysis to identify the putative ST genes in Erianthus rufipilus (E. rufipilus) and in Saccharum officinarum (S. officinarum). We identified 78 ST gene families in E. rufipilus and 86 ST gene families in S. officinarum. Phylogenetic analysis distributed the ST genes into eight distinct subfamilies (INT, MST, VGT, pGlcT, PLT, STP, SFP and SUT). Chromosomal distribution of ST genes clustered them on 10 respective chromosomes. Furthermore, synteny analysis with S. spontaneum and Sorghum bicolor (S. bicolor) revealed highly colinear regions. Synonymous and non-synonymous ratio (Ka/Ks) showed purifying selection in gene evolution. Promoter analysis identified several cis-regulatory elements, mainly associated with light responsiveness. We also examined the expression pattern of ST genes in different developing tissues (mature leaf, pre-mature stem, mature stem and seedling stem). Under sugar stress, we identified the significant ST genes showing differential expression patterns. Moreover, our yeast one-hybrid (Y1H) assays identified NAM, ATAF and CUC (NAC) and Lesion Simulating Disease (LSD) potential transcription factors (TFs) that may bind to the SUT1-T1 promoter in S. officinarum, showing negative correlation pattern with SUT1-T1. Our results deepen our understanding of ST gene evolution in Saccharum species and will facilitate the future investigation of functional analysis of the ST gene family. |
| format | Article |
| id | doaj-art-2b286517c95a462b893bd2e3be6aa55a |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-2b286517c95a462b893bd2e3be6aa55a2025-01-09T10:42:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.15026491502649Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factorsSehrish Akbar0Xuiting Hua1Yingying Zhang2Gang Liu3Tianyou Wang4Huihong Shi5Zhen Li6Yiying Qi7Habiba Habiba8Wei Yao9Mu-Qing Zhang10Jisen Zhang11Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaCenter for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaCenter for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaCenter for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaCenter for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaDepartment of Biological Science, Lehman College, City University of New York, Bronx, NY, United StatesState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, ChinaSugar, the primary product of photosynthesis, is a vital requirement for cell activities. Allocation of sugar from source to sink tissues is facilitated by sugar transporters (ST). These STs belong to the Major Facilitator Superfamily (MFS), the largest family of STs in plants. In this study, we performed genome wide and gene expression data analysis to identify the putative ST genes in Erianthus rufipilus (E. rufipilus) and in Saccharum officinarum (S. officinarum). We identified 78 ST gene families in E. rufipilus and 86 ST gene families in S. officinarum. Phylogenetic analysis distributed the ST genes into eight distinct subfamilies (INT, MST, VGT, pGlcT, PLT, STP, SFP and SUT). Chromosomal distribution of ST genes clustered them on 10 respective chromosomes. Furthermore, synteny analysis with S. spontaneum and Sorghum bicolor (S. bicolor) revealed highly colinear regions. Synonymous and non-synonymous ratio (Ka/Ks) showed purifying selection in gene evolution. Promoter analysis identified several cis-regulatory elements, mainly associated with light responsiveness. We also examined the expression pattern of ST genes in different developing tissues (mature leaf, pre-mature stem, mature stem and seedling stem). Under sugar stress, we identified the significant ST genes showing differential expression patterns. Moreover, our yeast one-hybrid (Y1H) assays identified NAM, ATAF and CUC (NAC) and Lesion Simulating Disease (LSD) potential transcription factors (TFs) that may bind to the SUT1-T1 promoter in S. officinarum, showing negative correlation pattern with SUT1-T1. Our results deepen our understanding of ST gene evolution in Saccharum species and will facilitate the future investigation of functional analysis of the ST gene family.https://www.frontiersin.org/articles/10.3389/fpls.2024.1502649/fullsugar transportergenome wide analysisErianthus rufipilusgene family analysisSaccharum officinarumyeast-1-hybrid (Y1H) assay |
| spellingShingle | Sehrish Akbar Xuiting Hua Yingying Zhang Gang Liu Tianyou Wang Huihong Shi Zhen Li Yiying Qi Habiba Habiba Wei Yao Mu-Qing Zhang Jisen Zhang Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors Frontiers in Plant Science sugar transporter genome wide analysis Erianthus rufipilus gene family analysis Saccharum officinarum yeast-1-hybrid (Y1H) assay |
| title | Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors |
| title_full | Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors |
| title_fullStr | Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors |
| title_full_unstemmed | Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors |
| title_short | Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors |
| title_sort | genome wide analysis of sugar transporter gene family in erianthus rufipilus and saccharum officinarum expression profiling and identification of transcription factors |
| topic | sugar transporter genome wide analysis Erianthus rufipilus gene family analysis Saccharum officinarum yeast-1-hybrid (Y1H) assay |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1502649/full |
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