Genome-Wide Identification and Analysis of SRO Gene Family in Chinese Cabbage (Brassica rapa L.)

Qiao, Yali; Gao, Xueqin; Liu, Zeci; Wu, Yue; Hu, Linli; Yu, Jiangnan

doi:10.3390/plants9091235

Cited by 9 publications

(8 citation statements)

References 43 publications

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“…Both cultivated and wild tomatoes SRO genes contained a large number of response elements, including gibberellin, ethylene, abscisic acid, jasmonic acid, and salicylic acid. SRO genes may affect tomato life activities by widely participating in hormone regulation networks, which is consistent with studies in other species ( YongChun et al, 2019 ; Qiao et al, 2020 ). There were also a large number of light-responsive CREs in the SRO promoter region, mainly BOX-4 and G-BOX, and most light-responsive elements were significantly enriched in S. lycopersicum var.…”

Section: Discussionsupporting

confidence: 87%

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Wang

et al. 2021

Front. Genet.

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SRO (SIMILAR TO RCD ONE) is a family of plant-specific small molecule proteins that play an important role in plant growth and development and environmental responses. However, SROs still lack systematic characterization in tomato. Based on bioinformatics methods, SRO family genes were identified and characterized from cultivated tomatoes and several wild tomatoes. qRT-PCR was used to study the expression of SRO gene in cultivated tomatoes. Phylogenetic and evolutionary analyses showed that SRO genes in angiosperms share a common ancestor and that the number of SRO family members changed as plants diverged and evolved. Cultivated tomato had six SRO members, five of which still shared some degree of identity with the ancestral SRO genes. Genetic structure and physicochemical properties showed that tomato SRO genes were highly conserved with chromosomal distribution. They could be divided into three groups based on exon-intron structure, and cultivated tomato contained only two of these subclades. A number of hormonal, light and abiotic stress-responsive cis-regulatory elements were identified from the promoter of the tomato SRO gene, and they also interacted with a variety of stress-responsive proteins and microRNAs. RNA-seq analysis showed that SRO genes were widely expressed in different tissues and developmental stages of tomato, with significant tissue-specific features. Expression analysis also showed that SRO genes respond significantly to high temperature and salt stress and mediate the tomato hormone regulatory network. These results provide a theoretical basis for further investigation of the functional expression of tomato SRO genes and provide potential genetic resources for tomato resistance breeding.

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Section: Discussionsupporting

confidence: 87%

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Wang

et al. 2021

Front. Genet.

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“…In recent years, a total of 5, 6, 6, 6, 12, and 30 SRO family genes have been identified in rice [ 6 , 21 ], apple [ 19 ], maize [ 22 ], banana [ 23 ], Chinese cabbage [ 24 ], wheat [ 25 ], and tomato [ 26 ], respectively. However, no relevant systematic study about the expression and possible roles of SRO genes in sesame, which has high nutritional quality, but its production is severely threatened by adverse environmental stresses [ 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

Liu

Wei

Zhou

et al. 2021

IJMS

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SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.

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“…In this study, the cucumber SRO family genes were identified and cloned, and these genes were named as CsSRO1-CsSRO4, making it a small gene family. The number of SRO family genes was compared to those of previously identified plant species, such as sesame, rice, Arabidopsis, maize, Brachypodium distachyon, tomato, banana, and apple, which generally contained 4-6 SRO genes in their genomes [46,[48][49][50], but was much less than that in Chinese cabbage (12 genes) [51], and wheat (30 genes) [45]. These findings indicated that the expansion of the SRO gene family was relatively conservative, and the number of SRO family genes may not possess an absolute correlation with genome size during plant evolution.…”

Section: Discussionmentioning

confidence: 99%

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

Xiao

ZHOU²,

Zhu³

et al. 2022

Horticulturae

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SIMILAR TO RCD-ONE (SRO) is a plant-specific small protein family that controls many biological processes including physiological development and stress responses. The SRO gene family has been studied in several plant species, but no detailed characterization and expression profiles of this important gene family were performed in cucumber. In this study, we characterize the SRO genes in cucumber, and determined their transcript levels in various tissues and under exposure to diverse biotic and abiotic stressors. Four SRO genes (named as CsSRO1–CsSRO4) were identified and isolated, which were distributed on three different chromosomes. Gene duplication analysis showed that only one pair of segmental duplication event was identified, but no tandem duplication events were detected. All CsSROs consist of the PARP domain and a C-terminal RST domain, while the N-terminal WWE domain was only present in CsSRO2 and CsSRO4. SROs from 15 plant species are divided into two groups (I and II), and group I can be further divided into four subgroups (Ia to Id) according to the phylogenetic tree. The conserved motif and gene structure analyses showed that SROs within the same branch of the phylogenetic tree have analogous conserved motifs configuration and gene structures. However, SRO genes possessed variable numbers of introns in different subgroups, which may affect the evolution of new family members. RNA-Seq data and qRT-PCR results showed that the four CsSRO genes have distinct expression pattern in various tissues and under diverse stresses, suggesting their multiple functions in plant growth and stress responses. The findings provide a basis for further research aiming at functional characterization of the regulatory mechanism to reveal the roles of CsSRO genes in developmental and stress-related processes of cucumber.

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Genome-Wide Identification and Analysis of SRO Gene Family in Chinese Cabbage (Brassica rapa L.)

Cited by 9 publications

References 43 publications

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

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