The Glutathione Peroxidase Gene Family in Gossypium hirsutum: Genome-Wide Identification, Classification, Gene Expression and Functional Analysis

Chen, Mingyang; Li, Kun; Li, Haipeng; Song, Chun‐Peng; Miao, Yuchen

doi:10.1038/srep44743

Cited by 69 publications

(68 citation statements)

References 53 publications

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“…Digital expression profiling is a particularly powerful and efficient method for large-scale gene-expression analysis [48][49][50][51][52][53][54][55], and it contributes to understanding gene functions. We therefore analyzed the expression profiles of the CIN gene family at different types of tissue and developmental stages from S. lycopersicum and S. tuberosum on the basis of in silico analysis (Figure 8).…”

Section: Cross-species Transcript Profiling Reveals High Constitutivementioning

confidence: 99%

Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum

Pan

Guo²,

Chai

et al. 2019

Biomolecules

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The invertase gene family in plants is composed of two subfamilies of enzymes, namely, acid-and neutral/alkaline invertases (cytosolic invertase, CIN). Both can irreversibly cleave sucrose into fructose and glucose, which are thought to play key roles in carbon metabolism and plant growth. CINs are widely found in plants, but little is reported about this family. In this paper, a comparative genomic approach was used to analyze the CIN gene family in Solanum, including Solanum tuberosum, Solanum lycopersicum, Solanum pennellii, Solanum pimpinellifolium, and Solanum melongena. A total of 40 CINs were identified in five Solanum plants, and sequence features, phylogenetic relationships, motif compositions, gene structure, collinear relationship, and expression profile were further analyzed. Sequence analysis revealed a remarkable conservation of CINs in sequence length, gene number, and molecular weight. The previously verified four amino acid residues (D188, E414, Arg430, and Ser547) were also observed in 39 out of 40 CINs in our study, showing to be deeply conserved. The CIN gene family could be distinguished into groups α and β, and α is further subdivided into subgroups α1 and α2 in our phylogenetic tree. More remarkably, each species has an average of four CINs in the α and β groups. Marked interspecies conservation and collinearity of CINs were also further revealed by chromosome mapping. Exon-intron configuration and conserved motifs were consistent in each of these α and β groups on the basis of in silico analysis. Expression analysis indicated that CINs were constitutively expressed and share similar expression profiles in all tested samples from S. tuberosum and S. lycopersicum. In addition, in CIN genes of the tomato and potato in response to abiotic and biotic stresses, phytohormones also performed. Overall, CINs in Solanum were encoded by a small and highly conserved gene family, possibly reflecting structural and functional conservation in Solanum. These results lay the foundation for further expounding the functional characterization of CIN genes and are also significant for understanding the evolutionary profiling of the CIN gene family in Solanum.

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Section: Cross-species Transcript Profiling Reveals High Constitutivementioning

confidence: 99%

Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum

Pan

Guo²,

Chai

et al. 2019

Biomolecules

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“…Recently, the availability of whole plant genome sequences provided an opportunity for identifying members of gene families [20][21][22][23]. Pepper is an important solanaceous vegetable crop, which has rich edible and medicinal value and is one of the most significant cash crops in China [24].…”

Section: Introductionmentioning

confidence: 99%

Sugar transporter proteins in Capsicum: identification, characterization, evolution and expression patterns

Wei

Liu

Zheng³

et al. 2020

Biotechnology & Biotechnological Equipment

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Sugar transporter proteins (STPs) play an important role in plant growth and development and stress resistance. Pepper (Capsicum annuum L.) is a significant economic crop and is widely cultivated worldwide. However, the evolution and the roles of STP genes in the growth and development and in coping with abiotic stresses in pepper are poorly known. Here, we characterized STP gene family in pepper through integration of chromosomal location, gene structure, conserved motif, phylogeny, expression patterns in different tissues and abiotic stresses. Using bioinformatics-based methods, we identified 17 putative STP genes in pepper. Chromosome mapping indicated that they are unevenly distributed on 9 chromosomes and there are tandem duplication events. Gene structure analysis revealed that intron numbers among these CaSTP genes ranged from 2 to 5, except that CaSTP12 and CaSTP13 genes contained no introns. The phylogenetic tree of STP genes from pepper and other plant species revealed that STP genes were grouped into 4 subfamilies, suggesting that these gene subfamilies may have diverged from a single common ancestor prior to the mono-dicot split. Gene expression analysis based on RNA-seq data showed that three genes were expressed constitutively in all the tissues analyzed, implying that these genes might have specific function in pepper. Stress data analysis showed that the expression profiles of some members of the CaSTP gene family were altered under cold, heat, salt and hormone stress conditions. The present results will provide valuable information into the evolutionary relationships and functional divergence of the STP family in the future. ARTICLE HISTORY

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“…Reactive oxygen species always act as important molecules and play pivotal roles in plant for abiotic stress (Chan, Yokawa, Kim, & Song, 2016; Li et al, 2018; Ma et al, 2011; Qi et al, 2018). Furthermore, ROS were also characterized as important signaling molecules that mediate plant hormone signaling transduction process, such as mitogen‐activated protein kinase (Wang, Du, Li, Ren, & Song, 2010; Wang, Du, Zhao, Miao, & Song, 2013) and hormone signaling (Chen, Li, Li, Song, & Miao, 2017; Dong, Wei, & Chen, 2013; Song, Miao, & Song, 2014). The activities of antioxidant enzymes, such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), were significantly changed under different light conditions in Camellia sinensis (Wu et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis

Wang

2020

Ecology and Evolution

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Solidago canadensis is an invasive plant that is capable of adapting to variable light conditions. To elucidate the shade tolerance mechanism in S. canadensis at the molecular level, transcriptome analyses were performed for leaves growing under natural light and three shade level conditions. Many differentially expressed genes (DEGs) were found in the comparative analysis, including those involved in photosynthesis, antioxidant, and secondary metabolism of phenol‐ and flavonoid‐related pathways. Most genes encoding proteins involved in photosynthesis, such as photosystem I reaction center subunit (Psa), photosystem II core complex protein (Psb), and light‐harvesting chlorophyll protein (Lhca and Lhcb), and reactive oxygen species (ROS) scavenging‐related enzymes, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were upregulated with the shade levels. Furthermore, most of the DEGs related to secondary metabolite synthesis were also upregulated in the shade conditions. Our study indicates that S. canadensis can respond to shade stress by modulating the expression of several photosynthesis‐related, free radical scavenging‐related, and secondary metabolism‐related genes; thus, this species has the ability to adapt to different light conditions.

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The Glutathione Peroxidase Gene Family in Gossypium hirsutum: Genome-Wide Identification, Classification, Gene Expression and Functional Analysis

Cited by 69 publications

References 53 publications

Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum

Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum

Sugar transporter proteins in Capsicum: identification, characterization, evolution and expression patterns

Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis

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