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Wang Y, Chen L, Yao Y, Chen L, Cui Y, An L, Li X, Bai Y, Yao X, Wu K. Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein-motif interaction in Qingke. PeerJ 2024; 12:e17736. [PMID: 39006012 PMCID: PMC11246018 DOI: 10.7717/peerj.17736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/23/2024] [Indexed: 07/16/2024] Open
Abstract
Background Currently, there are no reports on the HvbHLH gene family in the recent barley genome (Morex_V3). Furthermore, the structural genes related to anthocyanin synthesis that interact with HvANT2 have yet to be fully identified. Methods In this study, a bioinformatics approach was used to systematically analyze the HvbHLH gene family. The expression of this gene family was analyzed through RNA sequencing (RNA-seq), and the gene with the most significant expression level, HvANT2, was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in different tissues of two differently colored varieties. Finally, structural genes related to anthocyanin synthesis and their interactions with HvANT2 were verified using a yeast one-hybrid (Y1H) assay. Results The study identified 161 bHLH genes, designated as HvbHLH1 to HvbHLH161, from the most recent barley genome available. Evolutionary tree analysis categorized barley bHLH TFs into 21 subfamilies, demonstrating a pronounced similarity to rice and maize. Through RNA-Seq analysis of purple and white grain Qingke, we discovered a significant transcription factor (TF), HvANT2 (HvbHLH78), associated with anthocyanin biosynthesis. Subsequently, HvANT2 protein-motifs interaction assays revealed 41 interacting motifs, three of which were validated through Y1H experiments. These validated motifs were found in the promoter regions of key structural genes (CHI, F3'H, and GT) integral to the anthocyanin synthesis pathway. These findings provide substantial evidence for the pivotal role of HvANT2 TF in anthocyanin biosynthesis.
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Affiliation(s)
- Yan Wang
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Lin Chen
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Youhua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Lupeng Chen
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Yongmei Cui
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Likun An
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Xin Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Yixiong Bai
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Xiaohua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
| | - Kunlun Wu
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
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Wang Y, Yao Y, Cui Y, An L, Li X, Bai Y, Ding B, Yao X, Wu K. Unveiling the mysteries of HvANS: a study on anthocyanin biosynthesis in qingke (hordeum vulgare L. var. Nudum hook. f.) seeds. BMC PLANT BIOLOGY 2024; 24:637. [PMID: 38971739 PMCID: PMC11227189 DOI: 10.1186/s12870-024-05364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Based on our previous research, a full-length cDNA sequence of HvANS gene was isolated from purple and white Qingke. The open reading frame (ORF) in the purple variety Nierumuzha was 1320 base pairs (bp), encoding 439 amino acids, while the ORF in the white variety Kunlun 10 was 1197 bp, encoding 398 amino acids. A nonsynonymous mutation was found at the position of 1195 bp (T/C) in the coding sequence (CDS) of the HvANS gene. We carried out a series of studies to further clarify the relationship between the HvANS gene and anthocyanin synthesis in Qingke. RESULTS The conservative structural domain prediction results showed that the encoded protein belonged to the PLN03178 superfamily. Multiple comparisons showed that this protein had the highest homology with Hordeum vulgare, at 88.61%. The approximately 2000 bp promoter sequence of the HvANS gene was identical in both varieties. The real-time fluorescence PCR (qRT-PCR) results revealed that HvANS expression was either absent or very low in the roots, stems, leaves, and awns of Nierumuzha. In contrast, the HvANS expression was high in the seed coats and seeds of Nierumuzha. Likewise, in Kunlun 10, HvANS expression was either absent or very low, indicating a tissue-specific and variety-specific pattern for HvANS expression. The subcellular localization results indicated that HvANS was in the cell membrane. Metabolomic results indicated that the HvANS gene is closely related to the synthesis of three anthocyanin substances (Idaein chloride, Kinetin 9-riboside, and Cyanidin O-syringic acid). Yeast single hybridization experiments showed that the HvANS promoter interacted with HvANT1, which is the key anthocyanin regulatory protein. In a yeast two-hybrid experiment, we obtained two significantly different proteins (ZWY2020 and POMGNT2-like) and verified the results by qRT-PCR. CONCLUSIONS These results provide a basis for further studies on the regulatory mechanism of HvANS in the synthesis of anthocyanins in Qingke purple grains.
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Affiliation(s)
- Yan Wang
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Youhua Yao
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Yongmei Cui
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Likun An
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Xin Li
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Yixiong Bai
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Baojun Ding
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Xiaohua Yao
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China.
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China.
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China.
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China.
| | - Kunlun Wu
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China.
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai, China.
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, Qinghai, China.
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China.
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Tian Y, Liu X, Chen X, Wang B, Dong M, Chen L, Yang Z, Li Y, Sun H. Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry ( Vaccinium spp.) Fruit. Int J Mol Sci 2024; 25:4137. [PMID: 38673724 PMCID: PMC11050320 DOI: 10.3390/ijms25084137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
As a highly economic berry fruit crop, blueberry is enjoyed by most people and has various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids. To obtain more accurate and comprehensive transcripts, the full-length transcriptome of half-highbush blueberry (Vaccinium corymbosum/angustifolium cultivar Northland) obtained using single molecule real-time and next-generation sequencing technologies was reported for the first time. Overall, 147,569 consensus transcripts (average length, 2738 bp; N50, 3176 bp) were obtained. After quality control steps, 63,425 high-quality isoforms were obtained and 5030 novel genes, 3002 long non-coding RNAs, 3946 transcription factor genes (TFs), 30,540 alternative splicing events, and 2285 fusion gene pairs were identified. To better explore the molecular mechanism of flavonoid biosynthesis in mature blueberry fruit, an integrative analysis of the metabolome and transcriptome was performed on the exocarp, sarcocarp, and seed. A relatively complete biosynthesis pathway map of phenylpropanoids, flavonoids, and proanthocyanins in blueberry was constructed. The results of the joint analysis showed that the 228 functional genes and 42 TFs regulated 78 differentially expressed metabolites within the biosynthesis pathway of phenylpropanoids/flavonoids. O2PLS analysis results showed that the key metabolites differentially accumulated in blueberry fruit tissues were albireodelphin, delphinidin 3,5-diglucoside, delphinidin 3-O-rutinoside, and delphinidin 3-O-sophoroside, and 10 structural genes (4 Vc4CLs, 3 VcBZ1s, 1 VcUGT75C1, 1 VcAT, and 1 VcUGAT), 4 transporter genes (1 VcGSTF and 3 VcMATEs), and 10 TFs (1 VcMYB, 2 VcbHLHs, 4 VcWD40s, and 3 VcNACs) exhibited strong correlations with 4 delphinidin glycosides. These findings provide insights into the molecular mechanisms of flavonoid biosynthesis and accumulation in blueberry fruit.
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Affiliation(s)
- Youwen Tian
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China;
| | - Xinlei Liu
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
| | - Xuyang Chen
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
| | - Bowei Wang
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
| | - Mei Dong
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China;
| | - Li Chen
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
| | - Zhengsong Yang
- High Mountain Economic Plant Research Institute, Yunnan Academy of Agricultural Sciences, Lijiang 674110, China;
| | - Yadong Li
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
| | - Haiyue Sun
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (Y.T.); (X.L.); (X.C.); (B.W.); (L.C.)
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Meng L, Su H, Qu Z, Lu P, Tao J, Li H, Zhang J, Zhang W, Liu N, Cao P, Jin J. Genome-wide identification and analysis of WD40 proteins reveal that NtTTG1 enhances drought tolerance in tobacco (Nicotiana tabacum). BMC Genomics 2024; 25:133. [PMID: 38302866 PMCID: PMC10835901 DOI: 10.1186/s12864-024-10022-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND WD40 proteins, which are highly prevalent in eukaryotes, play important roles in plant development and stress responses. However, systematic identification and exploration of WD40 proteins in tobacco have not yet been conducted. RESULTS In this study, a total of 399 WD40 regulatory genes were identified in common tobacco (Nicotiana tabacum). Gene structure and motif analysis revealed structural and functional diversity among different clades of tobacco WD40 regulatory genes. The expansion of tobacco WD40 regulatory genes was mainly driven by segmental duplication and purifying selection. A potential regulatory network of NtWD40s suggested that NtWD40s might be regulated by miRNAs and transcription factors in various biological processes. Expression pattern analysis via transcriptome analysis and qRT-PCR revealed that many NtWD40s exhibited tissue-specific expression patterns and might be involved in various biotic and abiotic stresses. Furthermore, we have validated the critical role of NtTTG1, which was located in the nuclei of trichome cells, in enhancing the drought tolerance of tobacco plants. CONCLUSIONS Our study provides comprehensive information to better understand the evolution of WD40 regulatory genes and their roles in different stress responses in tobacco.
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Grants
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- CNTC: 110202101008(JY-08), 110202201001(JY-01), 110202202038 the Zhengzhou Tobacco Research Institute
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
- 232300420220 Natural Science Foundation of HeNan
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Affiliation(s)
- Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Huan Su
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Zechao Qu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - He Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Wei Zhang
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Nan Liu
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy, Beijing, 102200, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
- Beijing Life Science Academy, Beijing, 102200, China.
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Mao J, Gao Z, Wang X, Lin M, Chen L, Ning X. Combined Widely Targeted Metabolomic, Transcriptomic, and Spatial Metabolomic Analysis Reveals the Potential Mechanism of Coloration and Fruit Quality Formation in Actinidia chinensis cv. Hongyang. Foods 2024; 13:233. [PMID: 38254533 PMCID: PMC10814455 DOI: 10.3390/foods13020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Postharvest kiwifruit (Actinidia chinensis cv. Hongyang) pulp is mainly composed of outer yellow-flesh (LR) and inner red-flesh (HR). However, information about the differences in coloration and fruit quality between these two parts are limited. In this study, widely targeted metabolomic, transcriptomic, and spatial metabolomic analyses were used to reveal the potential mechanism of coloration and fruit quality formation. The results show that a total of 1001 metabolites were identified in Hongyang kiwifruit, and the accumulation of 211 metabolites were significantly higher in the HR than LR, including 69 flavonoids, 53 phenolic acids, and 38 terpenoids. There were no significant differences in the content of citric acid, quinic acid, glucose, fructose, or sucrose between the LR and HR. These results were consistent with the results from the RNA-seq profile and spatial metabolomic analysis. In addition, a total of 23 key candidate genes related to flesh color and fruit quality formation were identified and validated by qRT-PCR analysis. This study provides a theoretical basis for elucidating the underlying mechanism of the formation of kiwifruit flesh color and fruit quality.
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Affiliation(s)
- Jipeng Mao
- Jiangxi Kiwifruit Engineering Research Center, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China; (J.M.)
| | - Zhu Gao
- Jiangxi Kiwifruit Engineering Research Center, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China; (J.M.)
| | - Xiaoling Wang
- Jiangxi Kiwifruit Engineering Research Center, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China; (J.M.)
| | - Mengfei Lin
- Jiangxi Kiwifruit Engineering Research Center, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China; (J.M.)
| | - Lu Chen
- Jinggangshan Institute of Biotechnology, Jiangxi Academy of Sciences, Ji’an 343009, China;
| | - Xinyi Ning
- College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang 330063, China
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Rao X, Qian Z, Xie L, Wu H, Luo Q, Zhang Q, He L, Li F. Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus. Genes (Basel) 2023; 14:2128. [PMID: 38136950 PMCID: PMC10743048 DOI: 10.3390/genes14122128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.
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Affiliation(s)
- Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Linyan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Huaying Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Quan Luo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Qiyue Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Lilian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.R.); (Z.Q.); (L.X.); (H.W.); (Q.L.); (Q.Z.)
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Kunming 650201, China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
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Kang JE, Jun JH, Kwon JH, Lee JH, Hwang K, Kim S, Jeong N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes (Basel) 2023; 14:1476. [PMID: 37510380 PMCID: PMC10379056 DOI: 10.3390/genes14071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein-nucleic acid interaction (PNI) and protein-protein interaction (PPI) analysis based on domain-domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain-motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms.
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Affiliation(s)
- Jee Eun Kang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ji Hae Jun
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Jung Hyun Kwon
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ju-Hyun Lee
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Kidong Hwang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Sungjong Kim
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Namhee Jeong
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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