Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis
The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. <i>Ipomoea aquatica<...
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| author | Zheng Liu Xiaoai Fu Hao Xu Yuxin Zhang Zhidi Shi Guangzhen Zhou Wenlong Bao |
| author_facet | Zheng Liu Xiaoai Fu Hao Xu Yuxin Zhang Zhidi Shi Guangzhen Zhou Wenlong Bao |
| author_sort | Zheng Liu |
| collection | DOAJ |
| description | The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. <i>Ipomoea aquatica</i> is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed <i>I. aquatica</i>, purple-stemmed <i>I. aquatica</i> has extremely high contents of anthocyanins. However, the information on <i>bHLH</i> genes in <i>I. aquatica</i> and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 <i>bHLH</i> genes in the <i>I. aquatica</i> genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of <i>Arabidopsis thaliana</i> (AtbHLH). Of these, 129 <i>IabHLH</i> genes were unevenly distributed across 15 chromosomes, while 28 <i>IabHLH</i> genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within <i>IabHLH</i> genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the <i>IabHLH</i> gene family expansion. Transcriptome analysis showed that the expression levels of 13 <i>IabHLH</i> genes were significantly different between the two varieties. Of these, the <i>IabHLH027</i> had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed <i>I. aquatica</i> than that in green-stemmed <i>I. aquatica</i>. All upregulated DEGs in purple-stemmed <i>I. aquatica</i> exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including <i>IabHLH142</i>, <i>IabHLH057</i>, and <i>IabHLH043</i> determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring <i>IabHLH</i> function and facilitating the breeding of anthocyanin-rich functional varieties of <i>I. aquatica</i>. |
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| spelling | doaj.art-6f29ebd85f3047daac7c8cd368532a2d2023-11-17T11:37:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01246565210.3390/ijms24065652Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin BiosynthesisZheng Liu0Xiaoai Fu1Hao Xu2Yuxin Zhang3Zhidi Shi4Guangzhen Zhou5Wenlong Bao6Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaCollege of Tropical Crops, Hainan University, Haikou 570228, ChinaKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, ChinaThe basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. <i>Ipomoea aquatica</i> is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed <i>I. aquatica</i>, purple-stemmed <i>I. aquatica</i> has extremely high contents of anthocyanins. However, the information on <i>bHLH</i> genes in <i>I. aquatica</i> and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 <i>bHLH</i> genes in the <i>I. aquatica</i> genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of <i>Arabidopsis thaliana</i> (AtbHLH). Of these, 129 <i>IabHLH</i> genes were unevenly distributed across 15 chromosomes, while 28 <i>IabHLH</i> genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within <i>IabHLH</i> genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the <i>IabHLH</i> gene family expansion. Transcriptome analysis showed that the expression levels of 13 <i>IabHLH</i> genes were significantly different between the two varieties. Of these, the <i>IabHLH027</i> had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed <i>I. aquatica</i> than that in green-stemmed <i>I. aquatica</i>. All upregulated DEGs in purple-stemmed <i>I. aquatica</i> exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including <i>IabHLH142</i>, <i>IabHLH057</i>, and <i>IabHLH043</i> determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring <i>IabHLH</i> function and facilitating the breeding of anthocyanin-rich functional varieties of <i>I. aquatica</i>.https://www.mdpi.com/1422-0067/24/6/5652gene familycis-acting elementgene duplication eventsevolutionary relationshipgene expression |
| spellingShingle | Zheng Liu Xiaoai Fu Hao Xu Yuxin Zhang Zhidi Shi Guangzhen Zhou Wenlong Bao Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis International Journal of Molecular Sciences gene family cis-acting element gene duplication events evolutionary relationship gene expression |
| title | Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis |
| title_full | Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis |
| title_fullStr | Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis |
| title_full_unstemmed | Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis |
| title_short | Comprehensive Analysis of bHLH Transcription Factors in <i>Ipomoea aquatica</i> and Its Response to Anthocyanin Biosynthesis |
| title_sort | comprehensive analysis of bhlh transcription factors in i ipomoea aquatica i and its response to anthocyanin biosynthesis |
| topic | gene family cis-acting element gene duplication events evolutionary relationship gene expression |
| url | https://www.mdpi.com/1422-0067/24/6/5652 |
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