Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)
Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut ge...
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Frontiers Media S.A.
2021-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.632509/full |
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| author | Wei Zhao Wei Zhao Yonghui Liu Yonghui Liu Lin Li Lin Li Haijun Meng Haijun Meng Ying Yang Ying Yang Zhaobin Dong Lei Wang Lei Wang Guoliang Wu Guoliang Wu |
| author_facet | Wei Zhao Wei Zhao Yonghui Liu Yonghui Liu Lin Li Lin Li Haijun Meng Haijun Meng Ying Yang Ying Yang Zhaobin Dong Lei Wang Lei Wang Guoliang Wu Guoliang Wu |
| author_sort | Wei Zhao |
| collection | DOAJ |
| description | Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut. |
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| language | English |
| last_indexed | 2024-12-22T05:38:38Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-64095a35fca940a2b41b935aebbd15492022-12-21T18:37:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-02-011210.3389/fgene.2021.632509632509Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)Wei Zhao0Wei Zhao1Yonghui Liu2Yonghui Liu3Lin Li4Lin Li5Haijun Meng6Haijun Meng7Ying Yang8Ying Yang9Zhaobin Dong10Lei Wang11Lei Wang12Guoliang Wu13Guoliang Wu14College of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaShangluo Shengda Industrial Co., Ltd., Luonan, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaCollege of Horticulture, Henan Agricultural University, Zhengzhou, ChinaHenan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, ChinaBasic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.https://www.frontiersin.org/articles/10.3389/fgene.2021.632509/fullred walnutbHLH transcription factorsanthocyanin biosynthesisgenome-wide identificationgene expression |
| spellingShingle | Wei Zhao Wei Zhao Yonghui Liu Yonghui Liu Lin Li Lin Li Haijun Meng Haijun Meng Ying Yang Ying Yang Zhaobin Dong Lei Wang Lei Wang Guoliang Wu Guoliang Wu Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) Frontiers in Genetics red walnut bHLH transcription factors anthocyanin biosynthesis genome-wide identification gene expression |
| title | Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) |
| title_full | Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) |
| title_fullStr | Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) |
| title_full_unstemmed | Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) |
| title_short | Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.) |
| title_sort | genome wide identification and characterization of bhlh transcription factors related to anthocyanin biosynthesis in red walnut juglans regia l |
| topic | red walnut bHLH transcription factors anthocyanin biosynthesis genome-wide identification gene expression |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.632509/full |
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