Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.)

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

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Genome-wide identification and expression analysis of the YUCCA gene family in soybean (Glycine max L.)

Plant Growth Regulation ◽

10.1007/s10725-016-0203-x ◽

2016 ◽

Vol 81 (2) ◽

pp. 265-275 ◽

Cited By ~ 6

Author(s):

Yuange Wang ◽

Huaihua Liu ◽

Shuping Wang ◽

Hongjie Li

Keyword(s):

Glycine Max ◽

Gene Family ◽

Expression Analysis ◽

Genome Wide ◽

Glycine Max L

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Cadmium Treatment Alters the Expression of Five Genes at theCda1Locus in Two Soybean Cultivars [Glycine Max(L.) Merr]

The Scientific World JOURNAL ◽

10.1155/2014/979750 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Yi Wang ◽

Xue Xiao ◽

Tiequan Zhang ◽

Houyang Kang ◽

Jian Zeng ◽

...

Keyword(s):

Glycine Max ◽

Expression Patterns ◽

Cd Accumulation ◽

Life Process ◽

Expression Levels ◽

Soybean Cultivars ◽

Cadmium Treatment ◽

Glycine Max L ◽

Stems And Leaves

Westag 97 has larger capacity of Cd accumulation in roots which prevents Cd from translocating into stems and leaves; conversely, AC Hime has smaller capacity of Cd accumulation in roots; more Cd is transported into stems and leaves. The different capacity of Cd in roots between Westag 97 and AC Hime causes the different Cd concentration in seeds. Meanwhile, according to the different expression levels of RSTK, ISCP, and H+-ATPase between Westag 97 and AC Hime, RSTK may be involved in transporting Cd into stems and leaves; H+-ATPase may be correlated to the capacity of Cd accumulation in roots; and Cd caused some changes of fundamental life process which leaded to the different expression patterns of ISCP between Westag 97 and AC Hime.

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Cloning, mapping, and analyses of expression of the Em-like gene family in soybean [Glycine max (L). Merr.]

Theoretical and Applied Genetics ◽

10.1007/s001220050501 ◽

1997 ◽

Vol 94 (8) ◽

pp. 957-967 ◽

Cited By ~ 9

Author(s):

E. S. Calvo ◽

E. S. Wurtle ◽

R. C. Shoemaker

Keyword(s):

Glycine Max ◽

Gene Family ◽

Glycine Max L

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Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

International Journal of Molecular Sciences ◽

10.3390/ijms22168758 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8758

Author(s):

Jishuai Huang ◽

Qiannan Zhang ◽

Yurong He ◽

Wei Liu ◽

Yanghong Xu ◽

...

Keyword(s):

Gene Family ◽

Profile Analysis ◽

Binding Protein ◽

Expression Patterns ◽

Functional Characterization ◽

Limited Information ◽

Protein Motifs ◽

Biotic Stresses ◽

Enhancer Binding Protein ◽

Gene Structures

The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

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Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

International Journal of Molecular Sciences ◽

10.3390/ijms23010469 ◽

2021 ◽

Vol 23 (1) ◽

pp. 469

Author(s):

Kai Tong ◽

Xinyang Wu ◽

Long He ◽

Shiyou Qiu ◽

Shuang Liu ◽

...

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Expression Profiles ◽

Stomatal Closure ◽

Expression Patterns ◽

Family Members ◽

Triticum Aestivum L ◽

Free Calcium ◽

Cis Acting ◽

Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

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Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration

International Journal of Molecular Sciences ◽

10.3390/ijms21062188 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2188

Author(s):

Miaomiao Qin ◽

Jing Wang ◽

Tianyi Zhang ◽

Xiangyang Hu ◽

Rui Liu ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Control Group ◽

Binding Motif ◽

Isatis Indigotica ◽

Rate Limiting Step ◽

Genome Wide ◽

Transgenic Lines ◽

Gene Structures ◽

High Auxin

Auxin is one of the most critical hormones in plants. YUCCA (Tryptophan aminotransferase of Arabidopsis (TAA)/YUCCA) enzymes catalyze the key rate-limiting step of the tryptophan-dependent auxin biosynthesis pathway, from IPA (Indole-3-pyruvateacid) to IAA (Indole-3-acetic acid). Here, 13 YUCCA family genes were identified from Isatis indigotica, which were divided into four categories, distributing randomly on chromosomes (2n = 14). The typical and conservative motifs, including the flavin adenine dinucleotide (FAD)-binding motif and flavin-containing monooxygenases (FMO)-identifying sequence, existed in the gene structures. IiYUCCA genes were expressed differently in different organs (roots, stems, leaves, buds, flowers, and siliques) and developmental periods (7, 21, 60, and 150 days after germination). Taking IiYUCCA6-1 as an example, the YUCCA genes functions were discussed. The results showed that IiYUCCA6-1 was sensitive to PEG (polyethylene glycol), cold, wounding, and NaCl treatments. The over-expressed tobacco plants exhibited high auxin performances, and some early auxin response genes (NbIAA8, NbIAA16, NbGH3.1, and NbGH3.6) were upregulated with increased IAA content. In the dark, the contents of total chlorophyll and hydrogen peroxide in the transgenic lines were significantly lower than in the control group, with NbSAG12 downregulated and some delayed leaf senescence characteristics, which delayed the senescence process to a certain extent. The findings provide comprehensive insight into the phylogenetic relationships, chromosomal distributions, and expression patterns and functions of the YUCCA gene family in I. indigotica.

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Genome-wide analysis of the PHB gene family in Glycine max (L.) Merr.

Genes & Genomics ◽

10.1007/s13258-017-0580-1 ◽

2017 ◽

Vol 39 (10) ◽

pp. 1095-1106

Author(s):

Min Song ◽

Xiangyong Peng ◽

Caifu Du ◽

Lei Lei ◽

Tao Zhang ◽

...

Keyword(s):

Glycine Max ◽

Gene Family ◽

Genome Wide Analysis ◽

Genome Wide ◽

Glycine Max L

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Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽

10.3390/agronomy10121855 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1855

Author(s):

Dan Luo ◽

Ziqi Jia ◽

Yong Cheng ◽

Xiling Zou ◽

Yan Lv

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Sequence Similarity ◽

Expression Profiles ◽

Expression Patterns ◽

Chromosomal Distribution ◽

Brassica Napus L ◽

Oil Crops ◽

Genome Wide ◽

Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

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Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽

10.1186/s12864-019-6091-5 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Mengyuan Wei ◽

Aili Liu ◽

Yujuan Zhang ◽

Yong Zhou ◽

Donghua Li ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Leucine Zipper ◽

Expression Patterns ◽

Functional Characterization ◽

Genome Wide ◽

Gene Structures ◽

Relationship Of ◽

Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

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