Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.)
Abstract Background WD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) complexes associated with anthocyanin synthesis, but studies of Qingke barley...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-04-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09240-5 |
| _version_ | 1827970648475959296 |
|---|---|
| author | Lin Chen Yongmei Cui Youhua Yao Likun An Yixiong Bai Xin Li Xiaohua Yao Kunlun Wu |
| author_facet | Lin Chen Yongmei Cui Youhua Yao Likun An Yixiong Bai Xin Li Xiaohua Yao Kunlun Wu |
| author_sort | Lin Chen |
| collection | DOAJ |
| description | Abstract Background WD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) complexes associated with anthocyanin synthesis, but studies of Qingke barley are lacking. Results In this study, 164 barley HvWD40 genes were identified in the barley genome and were analyzed to determine their relevant bioinformatics. The 164 HvWD40 were classified into 11 clusters and 14 subfamilies based on their structural and phylogenetic protein profiles. Co-lineage analysis revealed that there were 43 pairs between barley and rice, and 56 pairs between barley and maize. Gene ontology (GO) enrichment analysis revealed that the molecular function, biological process, and cell composition were enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the RNA transport pathway was mainly enriched. Based on the identification and analysis of the barley WD40 family and the transcriptome sequencing (RNA-seq) results, we found that HvWD40-140 (WD40 family; Gene ID: r1G058730), HvANT1 (MYB family; Gene ID: HORVU7Hr1G034630), and HvANT2 (bHLH family; Gene ID: HORVU2Hr1G096810) were important components of the MBW complex related to anthocyanin biosynthesis in Qingke, which was verified via quantitative real-time fluorescence polymerase chain reaction (qRT-PCR), subcellular location, yeast two-hybrid (Y2H), and bimolecular fluorescent complimentary (BiFC) and dual-luciferase assay analyses. Conclusions In this study, we identified 164 HvWD40 genes in barley and found that HvnANT1, HvnANT2, and HvWD40-140 can form an MBW complex and regulate the transcriptional activation of the anthocyanin synthesis related structural gene HvDFR. The results of this study provide a theoretical basis for further study of the mechanism of HvWD40-140 in the MBW complex related to anthocyanin synthesis in Qingke. |
| first_indexed | 2024-04-09T18:57:05Z |
| format | Article |
| id | doaj.art-6b05529eac364d2c94ca8ea5ec626bc7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T18:57:05Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6b05529eac364d2c94ca8ea5ec626bc72023-04-09T11:08:48ZengBMCBMC Genomics1471-21642023-04-0124111510.1186/s12864-023-09240-5Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.)Lin Chen0Yongmei Cui1Youhua Yao2Likun An3Yixiong Bai4Xin Li5Xiaohua Yao6Kunlun Wu7Academy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAcademy of Agricultural and Forestry Sciences, Qinghai UniversityAbstract Background WD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) complexes associated with anthocyanin synthesis, but studies of Qingke barley are lacking. Results In this study, 164 barley HvWD40 genes were identified in the barley genome and were analyzed to determine their relevant bioinformatics. The 164 HvWD40 were classified into 11 clusters and 14 subfamilies based on their structural and phylogenetic protein profiles. Co-lineage analysis revealed that there were 43 pairs between barley and rice, and 56 pairs between barley and maize. Gene ontology (GO) enrichment analysis revealed that the molecular function, biological process, and cell composition were enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the RNA transport pathway was mainly enriched. Based on the identification and analysis of the barley WD40 family and the transcriptome sequencing (RNA-seq) results, we found that HvWD40-140 (WD40 family; Gene ID: r1G058730), HvANT1 (MYB family; Gene ID: HORVU7Hr1G034630), and HvANT2 (bHLH family; Gene ID: HORVU2Hr1G096810) were important components of the MBW complex related to anthocyanin biosynthesis in Qingke, which was verified via quantitative real-time fluorescence polymerase chain reaction (qRT-PCR), subcellular location, yeast two-hybrid (Y2H), and bimolecular fluorescent complimentary (BiFC) and dual-luciferase assay analyses. Conclusions In this study, we identified 164 HvWD40 genes in barley and found that HvnANT1, HvnANT2, and HvWD40-140 can form an MBW complex and regulate the transcriptional activation of the anthocyanin synthesis related structural gene HvDFR. The results of this study provide a theoretical basis for further study of the mechanism of HvWD40-140 in the MBW complex related to anthocyanin synthesis in Qingke.https://doi.org/10.1186/s12864-023-09240-5QingkeMBW complexHvWD40-140HvANT1HvANT2Anthocyanin |
| spellingShingle | Lin Chen Yongmei Cui Youhua Yao Likun An Yixiong Bai Xin Li Xiaohua Yao Kunlun Wu Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) BMC Genomics Qingke MBW complex HvWD40-140 HvANT1 HvANT2 Anthocyanin |
| title | Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) |
| title_full | Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) |
| title_fullStr | Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) |
| title_full_unstemmed | Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) |
| title_short | Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.) |
| title_sort | genome wide identification of wd40 transcription factors and their regulation of the myb bhlh wd40 mbw complex related to anthocyanin synthesis in qingke hordeum vulgare l var nudum hook f |
| topic | Qingke MBW complex HvWD40-140 HvANT1 HvANT2 Anthocyanin |
| url | https://doi.org/10.1186/s12864-023-09240-5 |
| work_keys_str_mv | AT linchen genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT yongmeicui genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT youhuayao genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT likunan genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT yixiongbai genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT xinli genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT xiaohuayao genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf AT kunlunwu genomewideidentificationofwd40transcriptionfactorsandtheirregulationofthemybbhlhwd40mbwcomplexrelatedtoanthocyaninsynthesisinqingkehordeumvulgarelvarnudumhookf |