Genome-wide identification, phylogeny, and expression profile of the sucrose transporter multigene family in tobacco

The transportation and distribution of sucrose in plants is mediated by sucrose transporters (SUTs), which also participate in various plant developmental and resistance processes. However, no such study of the tobacco SUT family has been reported yet. In the present study, 11, 5, and 4 SUT genes were identified from the genomes of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis, respectively. The exon–intron structures of the tobacco SUT genes were highly conserved in the three tobacco species. Gene loss, duplication, and chromosome exchange occurred in the NtSUT family during the formation of allotetraploid common tobacco. Expression profiling analysis revealed that the expression patterns of the NtSUT genes in common tobacco were closer to those in N. sylvestris plants. The NtSUT2s and NtSUT4 genes were ubiquitously expressed in various tobacco tissues, while the NtSUT1s gene was highly expressed in the maturing leaves, indicating their functional conservation and differentiation. The transcriptions of the NtSUT2t, NtSUT3s, NtSUT4, and NtSUT5s genes in tobacco plants were dramatically induced under Pi starvation, drought, and salinity stresses, but their highest expression levels occurred in different tissues, suggesting the multiple roles of NtSUTs in plant resistance to various abiotic stresses. This study provides useful information for the further functional characterization of SUT genes in tobacco.

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Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

10.20944/preprints202107.0311.v1 ◽

2021 ◽

Author(s):

Shefali Mishra ◽

Pradeep Sharma ◽

Rajender Singh ◽

ratan Tiwari ◽

Gyanendra Pratap Singh

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Structural Characteristics ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Functional Characterization ◽

Plant Stress ◽

Protein Motif ◽

Genome Wide

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

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Genome-wide identification and characterization of the ALOG gene family in Petunia

BMC Plant Biology ◽

10.1186/s12870-019-2127-x ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Feng Chen ◽

Qin Zhou ◽

Lan Wu ◽

Fei Li ◽

Baojun Liu ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Functional Characterization ◽

Reproductive Organs ◽

Genome Wide ◽

Domain Of Unknown Function ◽

Intron Structure ◽

Identification And Characterization ◽

Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

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

10.21203/rs.3.rs-17109/v1 ◽

2020 ◽

Author(s):

Weizhuo Zhu ◽

Dezhi Wu ◽

Lixi Jiang ◽

Lingzhen Ye

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Expression Patterns ◽

Functional Characterization ◽

Composition Analysis ◽

Distribution Analysis ◽

Element Analysis ◽

Genome Wide ◽

Identification And Characterization

Abstract 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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Functional conservation of erythropoietin signaling in zebrafish

Blood ◽

10.1182/blood-2006-04-016535 ◽

2007 ◽

Vol 110 (7) ◽

pp. 2718-2726 ◽

Cited By ~ 77

Author(s):

Noëlle Paffett-Lugassy ◽

Nelson Hsia ◽

Paula G. Fraenkel ◽

Barry Paw ◽

Irene Leshinsky ◽

...

Keyword(s):

Expression Patterns ◽

Functional Characterization ◽

Erythroid Progenitor ◽

Mature Erythrocyte ◽

Functional Conservation ◽

Hypoxic Conditions ◽

Definitive Erythropoiesis ◽

Mammalian Gene Expression

Erythropoietin (Epo) and its cognate receptor (EpoR) are required for maintaining adequate levels of circulating erythrocytes during embryogenesis and adulthood. Here, we report the functional characterization of the zebrafish epo and epor genes. The expression of epo and epor was evaluated by quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization, revealing marked parallels between zebrafish and mammalian gene expression patterns. Examination of the hypochromic mutant, weissherbst, and adult hypoxia-treated hearts indicate that zebrafish epo expression is induced by anemia and hypoxia. Overexpression of epo mRNA resulted in severe polycythemia, characterized by a striking increase in the number of cells expressing scl, c-myb, gata1, ikaros, epor, and βe1-globin, suggesting that both the erythroid progenitor and mature erythrocyte compartments respond to epo. Morpholino-mediated knockdown of the epor caused a slight decrease in primitive and complete block of definitive erythropoiesis. Abrogation of STAT5 blocked the erythropoietic expansion by epo mRNA, consistent with a requirement for STAT5 in epo signaling. Together, the characterization of zebrafish epo and epor demonstrates the conservation of an ancient program that ensures proper red blood cell numbers during normal homeostasis and under hypoxic conditions.

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

10.21203/rs.3.rs-17109/v2 ◽

2020 ◽

Author(s):

Weizhuo Zhu ◽

Dezhi Wu ◽

Lixi Jiang ◽

Lingzhen Ye

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Expression Patterns ◽

Functional Characterization ◽

Composition Analysis ◽

Distribution Analysis ◽

Element Analysis ◽

Genome Wide ◽

Identification And Characterization

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Genome-wide identification of GMP genes in Rosaceae and functional characterization of FaGMP4 in strawberry (Fragaria × ananassa)

Genes & Genomics ◽

10.1007/s13258-021-01062-7 ◽

2021 ◽

Author(s):

Yuanxiu Lin ◽

Jiahao Zhang ◽

Lintai Wu ◽

Yunting Zhang ◽

Qing Chen ◽

...

Keyword(s):

Functional Characterization ◽

Fragaria Ananassa ◽

Genome Wide

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Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

BMC Plant Biology ◽

10.1186/s12870-020-02767-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yushan Liu ◽

Yizhou Wang ◽

Jiabo Pei ◽

Yadong Li ◽

Haiyue Sun

Keyword(s):

Gene Family ◽

Fruit Development ◽

Lignin Content ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Vaccinium Corymbosum ◽

Land Plant ◽

Phylogenetic Structure ◽

Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

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Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20225796 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5796

Author(s):

Qianqian Zhou ◽

Qingchang Li ◽

Peng Li ◽

Songtao Zhang ◽

Che Liu ◽

...

Keyword(s):

Gene Family ◽

Physiological Stress ◽

Expression Patterns ◽

Functional Characterization ◽

Hormone Treatment ◽

Nicotiana Sylvestris ◽

Regulatory Elements ◽

Evolutionary Analysis ◽

Comprehensive Overview ◽

Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

10.21203/rs.3.rs-36113/v3 ◽

2020 ◽

Author(s):

Yanan Song ◽

Hongli Cui ◽

Ying Shi ◽

Jinai Xue ◽

Chunli Ji ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Stress Resistance ◽

Segmental Duplication ◽

Functional Characterization ◽

High Stress ◽

Camelina Sativa ◽

Genome Wide ◽

Large Expansion

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

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