Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet
Abstract Objectives Pearl millet (Pennisetum glaucum) is a cereal crop that is tolerant to a high temperature, a drought and a nutrient-poor condition. Characterizing pearl millet proteins can help to improve productivity of pearl millet and other crops. Transcription factors in general are proteins...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13104-023-06305-2 |
| _version_ | 1797865672060960768 |
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| author | Yingwei Qu Ambika Dudhate Harshraj Subhash Shinde Tetsuo Takano Daisuke Tsugama |
| author_facet | Yingwei Qu Ambika Dudhate Harshraj Subhash Shinde Tetsuo Takano Daisuke Tsugama |
| author_sort | Yingwei Qu |
| collection | DOAJ |
| description | Abstract Objectives Pearl millet (Pennisetum glaucum) is a cereal crop that is tolerant to a high temperature, a drought and a nutrient-poor condition. Characterizing pearl millet proteins can help to improve productivity of pearl millet and other crops. Transcription factors in general are proteins that regulate transcription of their target genes and thereby regulate diverse processes. Some transcription factor families in pearl millet were characterized in previous studies, but most of them are not. The objective of the data presented was to characterize amino acid sequences for most transcription factors in pearl millet. Data description Sequences of 2395 pearl millet proteins that have transcription factor-associated domains were extracted. Subcellular and suborganellar localization of these proteins was predicted by MULocDeep. Conserved domains in these sequences were confirmed by CD-Search. These proteins were classified into 85 families on the basis of those conserved domains. A phylogenetic tree including pearl millet proteins and their counterparts in Arabidopsis thaliana and rice was constructed for each of these families. Sequence motifs were identified by MEME for each of these families. |
| first_indexed | 2024-04-09T23:11:56Z |
| format | Article |
| id | doaj.art-6144b13eea954ef491f3eb57320381e1 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-09T23:11:56Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-6144b13eea954ef491f3eb57320381e12023-03-22T10:20:08ZengBMCBMC Research Notes1756-05002023-03-011611310.1186/s13104-023-06305-2Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl milletYingwei Qu0Ambika Dudhate1Harshraj Subhash Shinde2Tetsuo Takano3Daisuke Tsugama4Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of TokyoStowers Institute for Medical ResearchUniversity of KentuckyAsian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of TokyoAsian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of TokyoAbstract Objectives Pearl millet (Pennisetum glaucum) is a cereal crop that is tolerant to a high temperature, a drought and a nutrient-poor condition. Characterizing pearl millet proteins can help to improve productivity of pearl millet and other crops. Transcription factors in general are proteins that regulate transcription of their target genes and thereby regulate diverse processes. Some transcription factor families in pearl millet were characterized in previous studies, but most of them are not. The objective of the data presented was to characterize amino acid sequences for most transcription factors in pearl millet. Data description Sequences of 2395 pearl millet proteins that have transcription factor-associated domains were extracted. Subcellular and suborganellar localization of these proteins was predicted by MULocDeep. Conserved domains in these sequences were confirmed by CD-Search. These proteins were classified into 85 families on the basis of those conserved domains. A phylogenetic tree including pearl millet proteins and their counterparts in Arabidopsis thaliana and rice was constructed for each of these families. Sequence motifs were identified by MEME for each of these families.https://doi.org/10.1186/s13104-023-06305-2Pearl milletTranscription factorPhylogenetic analysisProtein familySubcellular localizationProtein domain |
| spellingShingle | Yingwei Qu Ambika Dudhate Harshraj Subhash Shinde Tetsuo Takano Daisuke Tsugama Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet BMC Research Notes Pearl millet Transcription factor Phylogenetic analysis Protein family Subcellular localization Protein domain |
| title | Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| title_full | Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| title_fullStr | Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| title_full_unstemmed | Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| title_short | Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| title_sort | phylogenetic trees conserved motifs and predicted subcellular localization for transcription factor families in pearl millet |
| topic | Pearl millet Transcription factor Phylogenetic analysis Protein family Subcellular localization Protein domain |
| url | https://doi.org/10.1186/s13104-023-06305-2 |
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