The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s
WD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (<i>Solanum tuberosum</i> L.). In the prese...
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MDPI AG
2020-03-01
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| Series: | Agronomy |
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| author | Zhen Liu Yuhui Liu Jeffrey A. Coulter Baoyun Shen Yuanming Li Chaozhou Li Zhengpeng Cao Junlian Zhang |
| author_facet | Zhen Liu Yuhui Liu Jeffrey A. Coulter Baoyun Shen Yuanming Li Chaozhou Li Zhengpeng Cao Junlian Zhang |
| author_sort | Zhen Liu |
| collection | DOAJ |
| description | WD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (<i>Solanum tuberosum</i> L.). In the present study, 178 potato WD40 (<i>StWD40</i>) genes were identified and their distribution on chromosomes, gene structure, and conserved motifs were assessed. According to their structural and phylogenetic protein features, these 178 <i>StWD40</i> genes were classified into 14 clusters and 10 subfamilies. Collinearity analysis showed that segmental duplication events played a major role in the expansion of the <i>StWD40</i> gene family. Synteny analysis indicated that 45 and 23 pairs of <i>StWD40</i> genes were orthologous to <i>Arabidopsis</i> and wheat (<i>Triticum aestivum</i>), respectively, and that these gene pairs evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-specific expression and abiotic stress-responsive <i>StWD40</i> genes in doubled monoploid potato (DM). Furthermore, we further analyzed the WD40 genes might be involved in anthocyanin biosynthesis and drought stress in tetraploid potato cultivars based on RNA-seq data. In addition, a protein interaction network of two homologs of <i>Arabidopsis TTG1</i>, which is involved in anthocyanin biosynthesis, was constructed to identify proteins that might be related to anthocyanin biosynthesis. The result showed that there were 112 pairs of proteins interacting with <i>TTG1</i>, with 27 being differentially expressed in pigmented tissues. This study indicates that WD40 proteins in potato might be related to anthocyanin biosynthesis and abiotic stress responses. |
| first_indexed | 2024-12-20T13:01:08Z |
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| language | English |
| last_indexed | 2024-12-20T13:01:08Z |
| publishDate | 2020-03-01 |
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| series | Agronomy |
| spelling | doaj.art-0c1ee98723b9482d8d112dfcf40325cb2022-12-21T19:39:54ZengMDPI AGAgronomy2073-43952020-03-0110340110.3390/agronomy10030401agronomy10030401The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40sZhen Liu0Yuhui Liu1Jeffrey A. Coulter2Baoyun Shen3Yuanming Li4Chaozhou Li5Zhengpeng Cao6Junlian Zhang7College of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaGansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, ChinaDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USAGansu Tiaoshan Institute of Agricultural and Forestry Science, Jingtai 730400, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaWD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (<i>Solanum tuberosum</i> L.). In the present study, 178 potato WD40 (<i>StWD40</i>) genes were identified and their distribution on chromosomes, gene structure, and conserved motifs were assessed. According to their structural and phylogenetic protein features, these 178 <i>StWD40</i> genes were classified into 14 clusters and 10 subfamilies. Collinearity analysis showed that segmental duplication events played a major role in the expansion of the <i>StWD40</i> gene family. Synteny analysis indicated that 45 and 23 pairs of <i>StWD40</i> genes were orthologous to <i>Arabidopsis</i> and wheat (<i>Triticum aestivum</i>), respectively, and that these gene pairs evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-specific expression and abiotic stress-responsive <i>StWD40</i> genes in doubled monoploid potato (DM). Furthermore, we further analyzed the WD40 genes might be involved in anthocyanin biosynthesis and drought stress in tetraploid potato cultivars based on RNA-seq data. In addition, a protein interaction network of two homologs of <i>Arabidopsis TTG1</i>, which is involved in anthocyanin biosynthesis, was constructed to identify proteins that might be related to anthocyanin biosynthesis. The result showed that there were 112 pairs of proteins interacting with <i>TTG1</i>, with 27 being differentially expressed in pigmented tissues. This study indicates that WD40 proteins in potato might be related to anthocyanin biosynthesis and abiotic stress responses.https://www.mdpi.com/2073-4395/10/3/401potato (<i>solanum tuberosum</i>)wd40 proteinexpression profilesanthocyanin biosynthesisdrought stress |
| spellingShingle | Zhen Liu Yuhui Liu Jeffrey A. Coulter Baoyun Shen Yuanming Li Chaozhou Li Zhengpeng Cao Junlian Zhang The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s Agronomy potato (<i>solanum tuberosum</i>) wd40 protein expression profiles anthocyanin biosynthesis drought stress |
| title | The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s |
| title_full | The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s |
| title_fullStr | The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s |
| title_full_unstemmed | The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s |
| title_short | The WD40 Gene Family in Potato (<i>Solanum Tuberosum</i> L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s |
| title_sort | wd40 gene family in potato i solanum tuberosum i l genome wide analysis and identification of anthocyanin and drought related wd40s |
| topic | potato (<i>solanum tuberosum</i>) wd40 protein expression profiles anthocyanin biosynthesis drought stress |
| url | https://www.mdpi.com/2073-4395/10/3/401 |
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