Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry
The plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s...
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MDPI AG
2020-04-01
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| Online Access: | https://www.mdpi.com/2073-4425/11/4/427 |
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| author | Yunting Zhang Yuyun Ye Leiyu Jiang Yuanxiu Lin Xianjie Gu Qing Chen Bo Sun Yong Zhang Ya Luo Yan Wang Xiaorong Wang Haoru Tang |
| author_facet | Yunting Zhang Yuyun Ye Leiyu Jiang Yuanxiu Lin Xianjie Gu Qing Chen Bo Sun Yong Zhang Ya Luo Yan Wang Xiaorong Wang Haoru Tang |
| author_sort | Yunting Zhang |
| collection | DOAJ |
| description | The plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s were identified from the strawberry genome database. They were respectively designated as FvSnRK1.1, FvSnRK2.1 to FvSnRK2.9 and FvSnRK3.1 to FvSnRK3.16, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. FvSnRK family members were unevenly distributed in seven chromosomes. The number of exons or introns varied among <i>FvSnRK1s</i>, <i>FvSnRK2s</i> and <i>FvSnRK3s</i>, but highly conserved in the same subfamily. The <i>FvSnRK1.1</i> had 10 exons. Most of <i>FvSnRK2s</i> had nine exons or eight introns, except <i>FvSnRK2.4</i>, <i>FvSnRK2.8</i> and <i>FvSnRK2.9</i>. <i>FvSnRK3</i> genes were divided into intron-free and intron-harboring members, and the number of introns in intron-harboring group ranged from 11 to 15. Moreover, the phylogenetic analysis showed SnRK1, SnRK2 and SnRK3 subfamilies respectively clustered together in spite of the different species of strawberry and Arabidopsis, indicating the genes were established prior to the divergence of the corresponding taxonomic lineages. Meanwhile, conserved motif analysis showed that FvSnRK sequences that belonged to the same subgroup contained their own specific motifs. Cis-element in promoter and expression pattern analyses of <i>FvSnRK1.1</i> suggested that <i>FvSnRK1.1</i> was involved in cold responsiveness, light responsiveness and fruit ripening. Taken together, this comprehensive analysis will facilitate further studies of the FvSnRK family and provide a basis for the understanding of their function in strawberry. |
| first_indexed | 2024-03-10T20:26:10Z |
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| id | doaj.art-6f5ca06b274343e7a033af14ac130c7c |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
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| spelling | doaj.art-6f5ca06b274343e7a033af14ac130c7c2023-11-19T21:45:19ZengMDPI AGGenes2073-44252020-04-0111442710.3390/genes11040427Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in StrawberryYunting Zhang0Yuyun Ye1Leiyu Jiang2Yuanxiu Lin3Xianjie Gu4Qing Chen5Bo Sun6Yong Zhang7Ya Luo8Yan Wang9Xiaorong Wang10Haoru Tang11College of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaMianyang Academy of Agricultural Sciences, Mianyang 621000, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaThe plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s were identified from the strawberry genome database. They were respectively designated as FvSnRK1.1, FvSnRK2.1 to FvSnRK2.9 and FvSnRK3.1 to FvSnRK3.16, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. FvSnRK family members were unevenly distributed in seven chromosomes. The number of exons or introns varied among <i>FvSnRK1s</i>, <i>FvSnRK2s</i> and <i>FvSnRK3s</i>, but highly conserved in the same subfamily. The <i>FvSnRK1.1</i> had 10 exons. Most of <i>FvSnRK2s</i> had nine exons or eight introns, except <i>FvSnRK2.4</i>, <i>FvSnRK2.8</i> and <i>FvSnRK2.9</i>. <i>FvSnRK3</i> genes were divided into intron-free and intron-harboring members, and the number of introns in intron-harboring group ranged from 11 to 15. Moreover, the phylogenetic analysis showed SnRK1, SnRK2 and SnRK3 subfamilies respectively clustered together in spite of the different species of strawberry and Arabidopsis, indicating the genes were established prior to the divergence of the corresponding taxonomic lineages. Meanwhile, conserved motif analysis showed that FvSnRK sequences that belonged to the same subgroup contained their own specific motifs. Cis-element in promoter and expression pattern analyses of <i>FvSnRK1.1</i> suggested that <i>FvSnRK1.1</i> was involved in cold responsiveness, light responsiveness and fruit ripening. Taken together, this comprehensive analysis will facilitate further studies of the FvSnRK family and provide a basis for the understanding of their function in strawberry.https://www.mdpi.com/2073-4425/11/4/427SnRKsphylogenetic analysisexpression patternstrawberry |
| spellingShingle | Yunting Zhang Yuyun Ye Leiyu Jiang Yuanxiu Lin Xianjie Gu Qing Chen Bo Sun Yong Zhang Ya Luo Yan Wang Xiaorong Wang Haoru Tang Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry Genes SnRKs phylogenetic analysis expression pattern strawberry |
| title | Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry |
| title_full | Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry |
| title_fullStr | Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry |
| title_full_unstemmed | Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry |
| title_short | Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry |
| title_sort | genome wide characterization of snf1 related protein kinases snrks and expression analysis of snrk1 1 in strawberry |
| topic | SnRKs phylogenetic analysis expression pattern strawberry |
| url | https://www.mdpi.com/2073-4425/11/4/427 |
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