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

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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Structure and Evolution of the Actin Gene Family in Arabidopsis thaliana

Genetics ◽

10.1093/genetics/142.2.587 ◽

1996 ◽

Vol 142 (2) ◽

pp. 587-602 ◽

Cited By ~ 8

Author(s):

John M McDowell ◽

Shurong Huang ◽

Elizabeth C McKinney ◽

Yong-Qiang An ◽

Richard B Meagher

Keyword(s):

Arabidopsis Thaliana ◽

Gene Family ◽

Higher Plants ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Gene Families ◽

Plant Evolution ◽

Actin Gene ◽

Specific Expression ◽

Phylogenetic Structure

Abstract Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.

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Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02872-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Kai Zhao ◽

Lin Liu ◽

...

Keyword(s):

Gene Family ◽

Higher Plants ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Regulatory Elements ◽

Late Embryogenesis Abundant ◽

Genome Wide ◽

Lea Gene ◽

Late Embryogenesis ◽

Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

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Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽

10.3390/agriculture11030244 ◽

2021 ◽

Vol 11 (3) ◽

pp. 244

Author(s):

Seung Hee Eom ◽

Tae Kyung Hyun

Keyword(s):

Functional Analysis ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Stress Responses ◽

Histone Deacetylases ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Gene Families ◽

Physiological Processes ◽

Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

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Unique and Overlapping Expression Patterns among the Arabidopsis 1-Amino-Cyclopropane-1-Carboxylate Synthase Gene Family Members

PLANT PHYSIOLOGY ◽

10.1104/pp.104.049999 ◽

2004 ◽

Vol 136 (2) ◽

pp. 2982-3000 ◽

Cited By ~ 236

Author(s):

Atsunari Tsuchisaka ◽

Athanasios Theologis

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Family Members

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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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A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

Royal Society Open Science ◽

10.1098/rsos.171463 ◽

2018 ◽

Vol 5 (7) ◽

pp. 171463 ◽

Cited By ~ 2

Author(s):

Yunpeng Cao ◽

Shumei Li ◽

Yahui Han ◽

Dandan Meng ◽

Chunyan Jiao ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Functional Divergence ◽

Sugar Content ◽

Expression Patterns ◽

Evolutionary Relationship ◽

World Market ◽

Pear Fruit ◽

Rosaceae Species ◽

Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

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Identification and genes expression analysis of ATP-dependent phosphofructokinase family members among three Saccharum species

Functional Plant Biology ◽

10.1071/fp12182 ◽

2013 ◽

Vol 40 (4) ◽

pp. 369 ◽

Cited By ~ 6

Author(s):

Lin Zhu ◽

Jisen Zhang ◽

Youqiang Chen ◽

Hongyu Pan ◽

Ray Ming

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Family Members ◽

Sucrose Metabolism ◽

Expression Level ◽

Group Iii ◽

Saccharum Species ◽

Subgroup Ii ◽

Unrooted Phylogenetic Tree ◽

Duplication Events

Sugarcane contributes ~80% of sugar production in the world and is an established biofuel crop. In working towards understanding the molecular basis of high sucrose accumulation, we have annotated and analysed the ATP-dependent phosphofructokinase (PFK) gene family that catalyses the phosphorylation of D-fructose 6-phosphate to D-fructose 1,6-bisphosphate. PFKs play an essential role in sucrose metabolism in plants and their expression patterns are unknown in sugarcane. In this study, based on the sorghum genome and sugarcane EST database, 10 PFK gene members were annotated and further verified by PCR using sugarcane genomic DNA. An unrooted phylogenetic tree was constructed with the deduced protein sequences of PFKs that were from the assembly of cDNA library of sugarcane and other plants. The results showed that gene duplication events and the retention rate after genome wide or segmental duplications occurred in higher frequency in monocots than in dicots and the genes in subgroup II of group III were likely originated from recent duplication events. Quantitative RT–PCR was performed to investigate the gene expression of 10 PFK genes in five tissues of three Saccharum species, including two developmental stages in leaves and three in culms. Of the PFK family members in sugarcane, ScPFK6, 7 and 8 appeared to be the primary isoforms based on the highly abundant expression of these three genes. ScPFK7 showed high expression level in the leaves, suggesting a potential role in sucrose metabolism. ScPFK8 had lower expression level in Saccharum officinarum L. than in the other two species, suggesting negative regulation of sucrose metabolism, which might have contributed to the high sugar content of S. officinarum. The genes in monocot specific subgroup II of group III, PFK7, 8 and 9, showed variation among the three Saccharum species, suggesting potential functional redundancy. Our results provide detailed annotation and analysis of the PFK gene family in sugarcane. Further elucidation of the role of ScPFK8 in the domestication process of sugarcane would be useful.

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Expression patterns ofBrassica napusgenes implicateIPT, CKX, sucrose transporter, cell wall invertase, and amino acid permease gene family members in leaf, flower, silique, and seed development

Journal of Experimental Botany ◽

10.1093/jxb/erv133 ◽

2015 ◽

Vol 66 (16) ◽

pp. 5067-5082 ◽

Cited By ~ 24

Author(s):

Jiancheng Song ◽

Lijun Jiang ◽

Paula Elizabeth Jameson

Keyword(s):

Cell Wall ◽

Amino Acid ◽

Gene Family ◽

Seed Development ◽

Expression Patterns ◽

Family Members ◽

Sucrose Transporter ◽

Cell Wall Invertase ◽

Amino Acid Permease

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Developmental and functional studies of the SLC12 gene family members from Drosophila melanogaster

AJP Cell Physiology ◽

10.1152/ajpcell.00376.2009 ◽

2010 ◽

Vol 298 (1) ◽

pp. C26-C37 ◽

Cited By ~ 23

Author(s):

Qifei Sun ◽

E. Tian ◽

R. James Turner ◽

Kelly G. Ten Hagen

Keyword(s):

Drosophila Melanogaster ◽

Gene Family ◽

Expression Patterns ◽

Family Members ◽

Specific Inhibitor ◽

Insect Cell Line ◽

Experimental Conditions ◽

Functional Studies ◽

Half Saturation Constant ◽

Late Embryogenesis

The electroneutral cation-chloride cotransporter gene family, SLC12, contains nine members in vertebrates. These include seven sodium and/or potassium-coupled chloride transporters and two membrane proteins of unknown function. Although SLC12 family members have been identified in a number of lower species, the functional properties of these proteins are unknown. There are five SLC12 homologues in Drosophila melanogaster , including at least one member on each of the four main branches of the vertebrate phylogenetic tree. We have employed in situ hybridization to study the expression patterns of the Drosophila SLC12 proteins during embryonic development. Our studies indicate that all five members of this family are expressed during early embryogenesis ( stages 1–6), but that spatial and temporal expression patterns become more refined as development proceeds. Expression during late embryogenesis was seen predominantly in the ventral nerve cord, salivary gland, gut, and anal pad. In parallel studies, we have carried out transport assays on each of the five Drosophila homologues, expressed as recombinant proteins in the cultured insect cell line High Five. Under our experimental conditions, we found that only one of these proteins, CG4357, transported the potassium congener 86Rb. Additional experiments established that rubidium transport via CG4357 was saturable ( Km = 0.29 ± 0.05 mM), sodium-dependent (half-saturation constant = 53 ± 11 mM), chloride-dependent (half-saturation constant = 48 ± 5 mM), and potently inhibited by bumetanide (inhibitor constant = 1.17 ± 0.08 μM), a specific inhibitor of Na+-K+-2Cl− cotransporters. Taken together, our results provide strong evidence that CG4357 is an insect ortholog of the vertebrate Na+-K+-2Cl− cotransporters.

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