Identification and expression profile analysis of the SnRK2 gene family in cucumber

Wan, Zilong; Luo, Shilei; Zhang, Zeyu; Liu, Zeci; Qiao, Yali; Gao, Xueqin; Yu, Jiangnan; Zhang, Guobin

doi:10.7717/peerj.13994

Cited by 4 publications

(5 citation statements)

References 76 publications

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“…The classification of the three gene families agrees with previous phylogenetic analyses in Arabidopsis, Brassica rapa , rice, tomato, banana, or cucumber [ 20 – 23 , 28 , 30 , 31 , 46 , 47 , 49 , 61 ]. Gene structure and protein motifs were also found to be conserved within members of the same family in C. sativus , rice and Gossypium ssp.…”

Section: Discussionsupporting

confidence: 87%

“…PYLs , PP2Cs and SnRK2s are encoded by multigene families with a variable number of genes among species. The number of CpPYL and CpSnRK2 genes in C. pepo (19 and 10, respectively) is similar to that of Arabidopsis (14 and 10) or cucumber (14 and 11) [ 23 , 46 , 49 ]. However, the number of CpPP2C genes was higher in C. pepo (102) than in Arabidopsis (80) or cucumber (56) [ 28 , 58 ], which is probably associated with duplication of the whole genome in Cucurbita [ 56 , 59 ], but also with the evolutionary diversification of the PP2C gene family to adapt plant species to multiple environments [ 28 , 60 ].…”

Section: Discussionmentioning

confidence: 97%

“…SnRK2 has been clustered into three subfamilies: subfamily I comprises kinases that are not activated by ABA; subfamily II comprises kinases that are not activated or are very weakly activated by ABA; and subfamily III comprises kinases strongly activated by ABA [ 45 ]. The SnRK2 family has been identified in many plant genomes, including 10 SnRK2 genes in Arabidopsis [ 46 ], 11 in banana [ 21 ], 10 in rice [ 47 ], 11 in maize [ 48 ], and 11 in cucumber [ 49 ]. Gene expression data and mutant characterization in several species have shown that the SnRK2 genes are an essential part of the ABA signalling pathway, at multiple stages of development and in response to abiotic stresses [ 50 – 52 ].…”

Section: Introductionmentioning

confidence: 99%

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Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

Iglesias-Moya,

Benítez,

Segura

et al. 2024

BMC Genomics

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Background The core regulation of the abscisic acid (ABA) signalling pathway comprises the multigenic families PYL, PP2C, and SnRK2. In this work, we conducted a genome-wide study of the components of these families in Cucurbita pepo. Results The bioinformatic analysis of the C. pepo genome resulted in the identification of 19 CpPYL, 102 CpPP2C and 10 CpSnRK2 genes. The investigation of gene structure and protein motifs allowed to define 4 PYL, 13 PP2C and 3 SnRK2 subfamilies. RNA-seq analysis was used to determine the expression of these gene families in different plant organs, as well as to detect their differential gene expression during germination, and in response to ABA and cold stress in leaves. The specific tissue expression of some gene members indicated the relevant role of some ABA signalling genes in plant development. Moreover, their differential expression under ABA treatment or cold stress revealed those ABA signalling genes that responded to ABA, and those that were up- or down-regulated in response to cold stress. A reduced number of genes responded to both treatments. Specific PYL-PP2C-SnRK2 genes that had potential roles in germination were also detected, including those regulated early during the imbibition phase, those regulated later during the embryo extension and radicle emergence phase, and those induced or repressed during the whole germination process. Conclusions The outcomes of this research open new research lines for agriculture and for assessing gene function in future studies.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

Iglesias-Moya,

Benítez,

Segura

et al. 2024

BMC Genomics

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“…Studies have shown that CYPC‐type GRX genes mainly encode detoxification and stress‐responsive proteins, while CGFS‐type GRX genes have protective effects against oxidative stress and are ubiquitous in diverse organisms (Li et al . 2007; Wan 2014). CC‐type GRX genes are unique to land plants and occur in much larger numbers than other types of GRX genes.…”

Section: Discussionmentioning

confidence: 99%

Identification and adaptive evolution analysis of glutaredoxin genes in Populus spp.

Wang,

Dong,

et al. 2023

Plant Biol J

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Glutaredoxin (GRX) is a class of small redox proteins widely involved in cellular redox homeostasis and the regulation of various cellular processes. The role of GRX gene in the differentiation of Populus spp. is rarely reported. We compared the similarities and differences of GRX genes among four sections of poplar using bioinformatics, corrected the annotations of some GRX genes, and focused on analysing their transcript profiling and adaptive evolution in Populus spp. A total of 219 GRX genes were identified in four sections of poplar, among which annotations for 13 genes were corrected. Differences in GRX genes were found between sect. Turanga, represented by P. euphratica, and other poplar sections. Most notably, P. euphratica had the smallest number of duplication events for GRX genes (n = 9) and no tandem duplications, whereas there were >25 duplication events for all other poplars. Furthermore, we detected 18 pairs of GRX genes under positive selection pressure in various sections of poplar, and identified two groups of GRX genes in the Salicaceae that potentially underwent positive selection. Expression profiling results showed that the PtrGRX34 and its orthologous genes were upregulated under stress treatments. In summary, the GRX gene family underwent expansion during poplar differentiation, and some genes underwent rapid evolution during this process, which may be beneficial for Populus spp. to adapt to environmental changes. This study may provide more insights into the molecular mechanisms of Populus spp. adaptation to environmental changes and the adaptive evolution of GRX genes.

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“…The FAR1/FHY3 protein sequences of cucumber, Arabidopsis and tomato were downloaded from the online database Ensembl [20]. The MEGA11 software (v2.010) was used to construct a phylogenetic tree of 61 FAR1/FHY3 protein sequences by applying the Maximum Likelihood method [25]. The bootstrap replication value was set as 1000, and the other parameters remained constant.…”

Section: Phylogenetic Analysis Of Cucumber Far1/fhy3 Genesmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of FAR1/FHY3 Gene Family in Cucumber (Cucumis sativus L.)

Li,

Qiao

et al. 2023

Agronomy

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The FAR1-RELATED SEQUENCE1 (FAR1) and FAR-RED ELONGATED HYPOCOTYL3 (FHY3) gene family plays a crucial role in various physiological and developmental processes, including seed germination, photomorphogenesis, flowering and stress responses. However, genome analysis of FAR1/FHY3 in cucumber (Cucumis sativus L.) has not been systemically investigated. In this study, 20 FAR1/FHY3 genes in cucumber were identified. The 20 FAR1/FHY3 members are randomly distributed on six chromosomes. The examination of subcellular localization indicated that the nucleus is the primary site where the 20 FAR1/FHY3 members are predominantly found. The analysis of the phylogenetic tree further revealed that the FAR1/FHY3 genes in cucumber are grouped into three distinct categories, exhibiting remarkable resemblance to the corresponding genes in other plant species. The analysis of cis-acting elements showed that most FAR1/FHY3 genes contain a variety of hormones as well as stress-related and light response elements. Through scrutinizing the expression patterns in various tissues, it was discerned that these genes are prominently expressed in roots, stems and leaves, with roots exhibiting the highest level of expression. Additionally, the 20 cucumber FAR1/FHY3 genes are all responsive to jasmonic acid methyl ester (Me-JA) and abscisic acid (ABA). CsFAR6 and CsFAR12 are significantly induced by Me-JA and ABA, respectively. CsFAR13 positively responds to NaCl and PEG6000 stresses. CsFAR11, CsFAR15 and CsFAR13 are significantly induced by the dark. The findings presented in this study establish compelling support for the potential involvement of FAR1/FHY3 genes in the growth, development and stress response of cucumbers. Moreover, these results serve as a solid basis for future investigations into the functional analysis of FAR1/FHY3.

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Identification and expression profile analysis of the SnRK2 gene family in cucumber

Cited by 4 publications

References 76 publications

Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

Identification and adaptive evolution analysis of glutaredoxin genes in Populus spp.

Genome-Wide Identification and Expression Analysis of FAR1/FHY3 Gene Family in Cucumber (Cucumis sativus L.)

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