Comprehensive Analysis of SnRK Gene Family and their Responses to Salt Stress in Eucalyptus grandis

Wang, Yujiao; Yan, Huifang; Zhenfei, Qiu; Hu, Bing; Zeng, Bo; Chen, Zhong; Fan, Chunjie

doi:10.3390/ijms20112786

Cited by 34 publications

(43 citation statements)

References 65 publications

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“…The number of exons or introns varied in different subfamilies and genes. The FvSnRK1.1 had 10 exons, which was the same as that reported for EgrSnRK1s and BdSnRK1s [25,26]. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9, which are consistent with that of most Arabidopsis, rice, maize, sorghum, tea and grape SnRK2 genes [27][28][29][30], suggesting that most SnRK2s in plants have a conserved structure with nine exons or eight introns.…”

Section: Discussionsupporting

confidence: 81%

“…As the plant has evolved, the subfamilies SnRK2 and SnRK3 have emerged, which are larger and relatively more diverse compared with SnRK1 [8]. Bioinformatic analysis of SnRK family has isolated a total of 39 AtSnRKs including three AtSnRK1s, 10 AtSnRK2s and 26 AtSnRK3s in Arabidopsis [21][22][23][24], 44 BdSnRKs including three BdSnRK1s, 10 BdSnRK2s and 31 BdSnRK3s in Brachypodium distachyon [25], 34 EgrSnRK including two EgrSnRK1s, eight EgrSnRK2s and 24 EgrSnRK3s in Eucalyptus grandis [26]. Here, we identified 26 FvSnRKs composed of one FvSnRK1, nine FvSnRK2s, 16 FvSnRK3s in the wild strawberry (Fragaria vesca).…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Zhang

Jiang

et al. 2020

Genes

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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.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Zhang

Jiang

et al. 2020

Genes

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“…Previous studies identi ed 39, 48, 44 and 34 SnRK genes in Arabidopsis thaliana (Hrabak et al, 2003), Oryza sativa (Kobayashi et al, 2004), Brachypodium distachyon (Wang et al, 2015) and Eucalyptus grandis (Wang et al, 2019), respectively. In B.napus genome, BnSnRK gene number is much higher than diplont plants.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of SnRK family genes in Brassica napus

Zhu

Jiang

et al. 2020

Preprint

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Background: Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.Results: Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.Conclusion: We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.

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“…LOC_Os03g03510 was found downregulated in DTY-IL. Both CIPK_C domain [ 110 ] and SnRK3 domain [ 111 , 112 ] have been implicated in abiotic stress responses, including drought tolerance. In addition, SnRK3, like SnRK1 [ 62 , 109 ] has been demonstrated to function in metabolic signaling and source-sink relationships.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.)

Tarun

Mauleon

Catausan

et al. 2020

Genes

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Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.

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Comprehensive Analysis of SnRK Gene Family and their Responses to Salt Stress in Eucalyptus grandis

Cited by 34 publications

References 65 publications

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Genome-wide identification and characterization of SnRK family genes in Brassica napus

Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.)

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