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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230852/ https://www.ncbi.nlm.nih.gov/pubmed/32316116 http://dx.doi.org/10.3390/genes11040427 |
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author | Zhang, Yunting Ye, Yuyun Jiang, Leiyu Lin, Yuanxiu Gu, Xianjie Chen, Qing Sun, Bo Zhang, Yong Luo, Ya Wang, Yan Wang, Xiaorong Tang, Haoru |
author_facet | Zhang, Yunting Ye, Yuyun Jiang, Leiyu Lin, Yuanxiu Gu, Xianjie Chen, Qing Sun, Bo Zhang, Yong Luo, Ya Wang, Yan Wang, Xiaorong Tang, Haoru |
author_sort | Zhang, Yunting |
collection | PubMed |
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 FvSnRK1s, FvSnRK2s and FvSnRK3s, but highly conserved in the same subfamily. The FvSnRK1.1 had 10 exons. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9. FvSnRK3 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 FvSnRK1.1 suggested that FvSnRK1.1 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. |
format | Online Article Text |
id | pubmed-7230852 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-72308522020-05-22 Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry Zhang, Yunting Ye, Yuyun Jiang, Leiyu Lin, Yuanxiu Gu, Xianjie Chen, Qing Sun, Bo Zhang, Yong Luo, Ya Wang, Yan Wang, Xiaorong Tang, Haoru Genes (Basel) Article 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 FvSnRK1s, FvSnRK2s and FvSnRK3s, but highly conserved in the same subfamily. The FvSnRK1.1 had 10 exons. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9. FvSnRK3 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 FvSnRK1.1 suggested that FvSnRK1.1 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. MDPI 2020-04-16 /pmc/articles/PMC7230852/ /pubmed/32316116 http://dx.doi.org/10.3390/genes11040427 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Yunting Ye, Yuyun Jiang, Leiyu Lin, Yuanxiu Gu, Xianjie Chen, Qing Sun, Bo Zhang, Yong Luo, Ya Wang, Yan Wang, Xiaorong Tang, Haoru Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in 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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230852/ https://www.ncbi.nlm.nih.gov/pubmed/32316116 http://dx.doi.org/10.3390/genes11040427 |
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