Transcriptome-Wide Identification and Characterization of the JAZ Gene Family in Mentha canadensis L.

Jasmonate ZIM-domain (JAZ) proteins are the crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and they play pervasive roles in plant development, defense, and plant specialized metabolism. Although numerous JAZ gene families have been discovered across several plants, our knowledge about the JAZ gene family remains limited in the economically and medicinally important Chinese herb Mentha canadensis L. Here, seven non-redundant JAZ genes named McJAZ1–McJAZ7 were identified from our reported M. canadensis transcriptome data. Structural, amino acid composition, and phylogenetic analysis showed that seven McJAZ proteins contained the typical zinc-finger inflorescence meristem (ZIM) domain and JA-associated (Jas) domain as conserved as those in other plants, and they were clustered into four groups (A-D) and distributed into five subgroups (A1, A2, B1, B2, and D). Quantitative real-time PCR (qRT-PCR) analysis showed that seven McJAZ genes displayed differential expression patterns in M. canadensis tissues, and preferentially expressed in flowers. Furthermore, the McJAZ genes expression was differentially induced after Methyl jasmonate (MeJA) treatment, and their transcripts were variable and up- or down-regulated under abscisic acid (ABA), drought, and salt treatments. Subcellular localization analysis revealed that McJAZ proteins are localized in the nucleus or cytoplasm. Yeast two-hybrid (Y2H) assays demonstrated that McJAZ1-5 interacted with McCOI1a, a homolog of Arabidopsis JA receptor AtCOI1, in a coronatine-dependent manner, and most of McJAZ proteins could also form homo- or heterodimers. This present study provides valuable basis for functional analysis and exploitation of the potential candidate McJAZ genes for developing efficient strategies for genetic improvement of M. canadensis.

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The maize hexokinase gene ZmHXK7 confers salt resistance in transgenic Arabidopsis plants

10.1101/2021.04.26.441367 ◽

2021 ◽

Author(s):

Qianqian Liu ◽

Zengyuan Tian ◽

Yuqi Guo

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Gene Family ◽

Transgenic Arabidopsis ◽

Expression Patterns ◽

Regulatory Elements ◽

Salt Resistance ◽

Pcr Analysis ◽

Plant Expression Vector ◽

Localization Analysis

AbstractThe hexokinase (HXK) gene family, whose members play vital roles in sugar induction signals and glycolysis in organisms, is widely found in plants. Although some hexokinase genes have been studied in maize, a systematic report of the gene family and its role in plant resistance is lacking. In this study, 10 hexokinase genes were systematically identified in maize based on the maize genome-wide database. Phylogenetic analysis divides the maize HXK protein family into four clusters. Prediction of cis-regulatory elements showed that a number of elements responding to abiotic stress exist in the promoter of hexokinase genes. The expression profile of these genes, originated from B73, showed that different members of hexokinase genes are highly expressed in roots and leaves of maize under salt or drought stress, which is similar to that of Mo17.The coding sequence of ZmHXK7 gene, isolated from maize B73, was constructed into plant expression vector pMDC45 and then transformed into athxk3 (Salk_022188C). By hyg resistance detection, PCR analysis, and western blot confirmation, the homozygous progenies of transgenic Arabidopsis lines were identified. Subcellular localization analysis showed that the ZmHXK7 gene was located in cytosol. Seedling growth and salt stress inhibition in complementary mutant plants of ZmHXK7 gene were significantly improved, and enhanced salt tolerance was displayed. Our study provides insights into the evolution and expression patterns of the hexokinase gene and show that maize ZmHXK7 proteins play an important role in resisting salt stress, which will be useful in plant breeding for abiotic stress resistance.

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Identification, Expression, and Functions of the Somatostatin Gene Family in Spotted Scat (Scatophagus argus)

Genes ◽

10.3390/genes11020194 ◽

2020 ◽

Vol 11 (2) ◽

pp. 194

Author(s):

Peizhe Feng ◽

Changxu Tian ◽

Xinghua Lin ◽

Dongneng Jiang ◽

Hongjuan Shi ◽

...

Keyword(s):

Gene Family ◽

Growth Regulation ◽

Expression Patterns ◽

Open Reading Frames ◽

Pcr Analysis ◽

Sequence Alignments ◽

Scatophagus Argus ◽

Gene Structure And Expression ◽

Liver Fragments

Somatostatins (SSTs) are a family of proteins consisting of structurally diverse polypeptides that play important roles in the growth regulation in vertebrates. In the present study, four somatostatin genes (SST1, SST3, SST5, and SST6) were identified and characterized in the spotted scat (Scatophagus argus). The open reading frames (ORFs) of SST1, SST3, SST5, and SST6 cDNA consist of 372, 384, 321, and 333 bp, respectively, and encode proteins of 123, 127, 106, and 110 amino acids, respectively. Amino acid sequence alignments indicated that all SST genes contained conserved somatostatin signature motifs. Real-time PCR analysis showed that the SST genes were expressed in a tissue specific manner. When liver fragments were cultured in vitro with synthetic peptides (SST1, SST2, or SST6 at 1 μM or 10 μM) for 3 h or 6 h, the expression of insulin-like growth factor 1 and 2 (Igf-1 and Igf-2) in the liver decreased significantly. Treatment with SST5 had no significant effect on Igf-1 and Igf-2 gene expression. This study provides an enhanced understanding of the gene structure and expression patterns of the SST gene family in S. argus. Furthermore, this study provides a foundation for future exploration into the role of SST genes in growth and development.

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Genome-Wide Identification and Expression Profiling Analysis of the Galactinol Synthase Gene Family in Cassava (Manihot esculenta Crantz)

Agronomy ◽

10.3390/agronomy8110250 ◽

2018 ◽

Vol 8 (11) ◽

pp. 250 ◽

Cited By ~ 4

Author(s):

Ruimei Li ◽

Shuai Yuan ◽

Yingdui He ◽

Jie Fan ◽

Yangjiao Zhou ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Manihot Esculenta ◽

Expression Patterns ◽

Pcr Analysis ◽

Systematic Research ◽

Raffinose Family Oligosaccharides ◽

Manihot Esculenta Crantz ◽

Galactinol Synthase ◽

Genome Wide

Galactinol synthases (GolSs) are the key enzymes that participate in raffinose family oligosaccharides (RFO) biosynthesis, which perform a big role in modulating plant growth and response to biotic or abiotic stresses. To date, no systematic study of this gene family has been conducted in cassava (Manihot esculenta Crantz). Here, eight MeGolS genes are isolated from the cassava genome. Based on phylogenetic background, the MeGolSs are clustered into four groups. Through predicting the cis-elements in their promoters, it was discovered that all MeGolS members act as hormone-, stress-, and tissue-specific related elements to different degrees. MeGolS genes exhibit incongruous expression patterns in various tissues, indicating that different MeGolS proteins might have diverse functions. MeGolS1 and MeGolS3–6 are highly expressed in leaves and midveins. MeGolS3–6 are highly expressed in fibrous roots. Quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis indicates that several MeGolSs, including MeGolS1, 2, 5, 6, and 7, are induced by abiotic stresses. microRNA prediction analysis indicates that several abiotic stress-related miRNAs target the MeGolS genes, such as mes-miR156, 159, and 169, which also respond to abiotic stresses. The current study is the first systematic research of GolS genes in cassava, and the results of this study provide a basis for further exploration the functional mechanism of GolS genes in cassava.

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Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

10.21203/rs.2.21019/v3 ◽

2020 ◽

Author(s):

Xiya Zuo ◽

Shixiang Wang ◽

Wen Xiang ◽

Huiru Yang ◽

Muhammad Mobeen Tahir ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Floral Transition ◽

Bimolecular Fluorescence Complementation ◽

Pcr Analysis ◽

Transcriptional Responses ◽

Genome Database ◽

Reverse Transcription Pcr ◽

Conserved Core

Abstract Background: Apple (Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

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Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

10.21203/rs.2.21019/v5 ◽

2020 ◽

Author(s):

Xiya Zuo ◽

Shixiang Wang ◽

Wen Xiang ◽

Huiru Yang ◽

Muhammad Mobeen Tahir ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Economic Value ◽

Floral Transition ◽

Bimolecular Fluorescence Complementation ◽

Pcr Analysis ◽

Transcriptional Responses ◽

Genome Database ◽

Reverse Transcription Pcr

Abstract Background: Apple (Malus domestica Borkh.) is a popular cultivated fruit crop with high economic value in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

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Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)

PeerJ ◽

10.7717/peerj.3955 ◽

2017 ◽

Vol 5 ◽

pp. e3955 ◽

Cited By ~ 16

Author(s):

Yiling Niu ◽

Tingting Zhao ◽

Xiangyang Xu ◽

Jingfu Li

Keyword(s):

Gene Family ◽

Solanum Lycopersicum ◽

Stress Responses ◽

Expression Patterns ◽

Gene Families ◽

Shoot Meristem ◽

Axillary Shoot ◽

Multiple Sequence ◽

Genome Wide ◽

First Time

Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.

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Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

10.21203/rs.2.22104/v1 ◽

2020 ◽

Author(s):

Yuxin Pan ◽

Jinpeng Wang ◽

Zhenyi Wang ◽

Hengwei Liu ◽

Lan Zhang ◽

...

Keyword(s):

Positive Selection ◽

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Subcellular Location ◽

Pcr Analysis ◽

Genome Wide ◽

Cotton Species ◽

Expressional Analysis ◽

Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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Genome-wide analysis of NAAT, DMAS, TOM, and ENA gene families in maize reveals their roles in regulating iron homeostasis

10.21203/rs.3.rs-19256/v1 ◽

2020 ◽

Author(s):

Xin Zhang ◽

Xiaojin Zhou ◽

Suzhen Li ◽

Jiaxing Huang ◽

Sen Pang ◽

...

Keyword(s):

Iron Deficiency ◽

Iron Homeostasis ◽

Expression Profiles ◽

Expression Patterns ◽

Genome Mining ◽

Gene Families ◽

Pcr Analysis ◽

Efflux Transporter ◽

Iron Starvation ◽

Maize Varieties

Abstract Background: Nicotianamine (NA) serves as not only the major chelator for iron transport but also the intermediate for synthesizing mugineic acid family phytosiderophores (MAs) which are secreted by graminaceous plants for Fe uptake. Therefore, the production and secretion of MAs are key steps for maintaining iron homeostasis in plants. Nicotianamine aminotransferase (NAAT), 2’-deoxymugineic acid synthase (DMAS), MAs efflux transporter (TOM), and efflux transporter of NA (ENA) were identified to be involved in these processes in rice and barley, whereas little systematic study has been performed in maize (Zea mays.L). Results: Here, we identified five ZmNAAT, nine ZmDMAS, eleven ZmTOM, and two ZmENA genes in maize by genome mining. RNA-sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) analysis revealed that the expression of these genes exhibited diverse tissue specificity and different responses to environmental iron conditions. Moreover, the expression patterns were related to their evolution relationships. In particular, the ZmNAAT family can be classified into two subgroups, with one group showed inhibited expression in root under iron excess status and another subclass were repressed in shoot under both iron deficiency and excess. Likewise, the expression of ZmDMAS1 was stimulated under iron deficiency, while the remaining genes fell into two sub-clades with different expression patterns. Significant up-regulation of ZmTOM1, ZmTOM3 and ZmENA1 were observed under iron starvation, while ZmTOM2 was induced under both iron-excess and deficiency. These results reflect changing demands for the synthesis and secretion of NA/MAs to balance iron homeostasis under fluctuating conditions. All the examined ZmNAAT and ZmDMAS proteins localized in cytoplasm, while plasma and tonoplast membrane, endomembrane, and vesicle localization were observed for ZmTOM and ZmENA proteins. These results indicate that ZmTOM and ZmENA proteins may contribute to not only intercellular export but also intracellular sequestration of NA and MAs to facilitate iron homeostasis. Conclusions: Our results suggest that different gene expression profiles and subcellular localization of ZmNAAT, ZmDMAS, ZmTOM, and ZmENA members may enable dedicate regulation of NA and phytosiderophores (PS) metabolism, shedding light on the understanding of iron-homeostasis in maize. Additionally, we also provided candidate genes for breeding iron-rich maize varieties.

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Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽

10.3390/f11030315 ◽

2020 ◽

Vol 11 (3) ◽

pp. 315

Author(s):

Hanzeng Wang ◽

Xue Leng ◽

Xuemei Xu ◽

Chenghao Li

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Interaction Network ◽

Pcr Analysis ◽

Phylogenetic Tree Analysis ◽

Element Analysis ◽

Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽

10.3390/plants9101356 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1356

Author(s):

Zhaohan Zhang ◽

Shahid Ali ◽

Tianxu Zhang ◽

Wanpeng Wang ◽

Linan Xie

Keyword(s):

Gene Family ◽

Higher Plants ◽

Expression Patterns ◽

Family Members ◽

Evolutionary Relationship ◽

Gene Families ◽

Class Iii ◽

Sequencing Data ◽

Entire Genome ◽

Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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