Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress

Büyük, İlker; Okay, Aybüke; Aras, Sümer

doi:10.1007/s10528-021-10108-0

Cited by 11 publications

(7 citation statements)

References 60 publications

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“…In eukaryotes, this is thought to ensue an early phase of relaxed constraint or even near-neutrality for diversification (Lynch & Conery, 2000), and possibly occurred during PK evolution due to their vital importance in diverse biological processes (Janitza et al, 2012). Both the presence of duplicated genes under purifying selection and the average Ka/Ks rate of common bean PKs (0.397) are concordant with previous findings from other gene families of this species, such as Dof (Ito et al, 2017), SBP transcription factors (Ilhan et al, 2018), CAMTA (Büyük et al, 2019), SRS (Büyük et al, 2022), and BURP domain-containing genes (Kavas et al, 2021). However, none of these studies – which analysed much smaller gene families – reported the high Ks values and distant dates of duplication we found for common bean PKs, dating up to 229 MYA.…”

Section: Discussionsupporting

confidence: 89%

“…Both the presence of duplicated genes under purifying selection and the average Ka/Ks rate of common bean PKs (0.397) are concordant with previous findings from other gene families of this species, such as Dof (Ito et al, 2017), SBP transcription factors (Ilhan et al, 2018), CAMTA (Büyük et al, 2019), SRS (Büyük et al, 2022), and BURP domain-containing genes (Kavas et al, 2021). However, none of these studies -which analysed much smaller gene families -reported the high Ks values and distant dates of duplication we found for common bean PKs, dating up to 229 MYA.…”

Section: Duplication Eventssupporting

confidence: 89%

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Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Aono

Pimenta

Kuroshu

et al. 2022

Preprint

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The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

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Section: Discussionsupporting

confidence: 89%

Section: Duplication Eventssupporting

confidence: 89%

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Aono

Pimenta

Kuroshu

et al. 2022

Preprint

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“…Meanwhile, research showed SRS genes are correlated with crop yields ( Kuusk et al, 2006 ). However, the identification of the SRS genes has been reported in maize, rice and Arabidopsis thaliana ( Kuusk et al, 2006 ; Yang et al, 2020 ; Yang et al, 2021 ; Büyük et al, 2022 ). It has not been reported in quinoa.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa

Zhu

Wang²,

Wang³

et al. 2022

Front. Genet.

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Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.

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“…Soybean ( Glycine max ) GmSRS18 has been shown to reduce drought and salt tolerance, as well as stress-related gene expression and physiological indicators such as chlorophyll, proline, and relative electrolyte leakage [ 17 ]. Due to their important regulatory function, an increasing number of SRS genes have been identified in various plant species in recent years, including rice ( O. Sativa ) [ 29 ], Z. mays [ 30 ], G. max [ 17 ], M. sativa [ 27 ], M. albus [ 28 ], and Phaseolus vulgaris [ 31 ]. Nevertheless, no genome-wide analysis of SRS family genes in cassava has been published.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

Huang

Song

Feng

et al. 2023

Genes

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The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

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Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress

Cited by 11 publications

References 60 publications

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

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