Preliminary Study Mechanism of Ethylene Induced Abscission Zone Formation and Function of GhArfGAP in Upland Cotton Boll Stalk

Abstract Background: With the continuous growth of population, the demand for fiber is also rising sharply. As one of the main fiber plants in the world, cotton fiber yield of upland cotton is affected by boll abscission, which is related to the formation of abscission zone. Therefore, we explored the formation of the abscission zone of upland cotton.Result: The formation of abscission layer of cotton boll stalk was promoted by exogenous ethylene. It was found that both the number of Golgi apparatus and the number of stacking layers increased in the dissociated cells. The GhArfGAP gene family in upland cotton was screened by bioinformatics method, and the species and evolutionary relationship of GhArfGAP gene family were analyzed. qRT-PCR showed that the expression patterns of GhArfGAP13,GhArfGAP15, GhArfGAP25 and GhArfGAP34 in cotton were spatiotemporal specific. Subcellular localization suggested that GhArfGAP25 played a role in Golgi apparatus . The expression of GhArfGAP25 in transgenic Arabidopsis increased in the root, stem and leaf.Conclusions: Ethylene could induce the formation of abscission zone in upland cotton. GhArfGAP13,GhArfGAP15,GhArfGAP25,GhArfGAP34 might regulate the changes of Golgi apparatus in abscisson zone.Taken together the findings provide new ideas for the study of cotton abscission formation.

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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, 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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Global insights into homoeolog gene expression in upland cotton under intraspecific hybridization

10.21203/rs.3.rs-234267/v1 ◽

2021 ◽

Author(s):

Kashif Shahzad ◽

Xuexian Zhang ◽

Meng Zhang ◽

Liping Guo ◽

Tingxiang Qi ◽

...

Keyword(s):

Gene Expression ◽

Upland Cotton ◽

Expression Patterns ◽

Yield Potential ◽

World Cotton ◽

Intraspecific Hybridization ◽

Genome Doubling ◽

Gene Pairs ◽

Agronomic Crops ◽

Metabolic Genes

Abstract Background: Hybridization is useful to enhance yield potential of agronomic crops in the world. Cotton has genome doubling due to alloteraploidy process and hybridization process in coordinate with duplicated genome can produce more yield and adaptability. Therefore, expression of homoeolog gene pairs between hybrids and inbred parents are vital to characterize genetic source of heterosis in cotton.Results: Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (An average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. Conclusions: These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.

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Genome-wide identification, phylogeny and expression analysis of G6PC gene family in common carp, Cyprinus carpio

Turkish Journal of Biochemistry ◽

10.1515/tjb-2018-0102 ◽

2020 ◽

Vol 45 (2) ◽

Author(s):

Sijia Liu ◽

Fei Tian ◽

Cunfang Zhang ◽

Zhigang Qiao ◽

Kai Zhao

Keyword(s):

Gene Family ◽

Common Carp ◽

Cyprinus Carpio ◽

Expression Profiles ◽

Expression Patterns ◽

Critical Role ◽

Cold Treatment ◽

Evolutionary Relationship ◽

Whole Genome Sequence ◽

Evolutionary Analysis

AbstractObjectiveThe Glucose 6-phosphatase (G6Pase) catalytic subunit (G6PC) catalyzes glucose 6-phosphate (G6P) to inorganic phosphate and glucose, playing a critical role in endogenous energy supply. Here, the G6PC gene family was investigated and characterized in common carp (Cyprinus carpio).MethodsSequence alignment and phylogenetic analysis were performed using MEGA5. The HMM profiles, motif structure were analyzed using Pfam and MEME, respectively. Quantitative real-time PCR was used to test the expression profiles.ResultsFour assumptive members of G6PC family in common carp whole-genome sequence were identified as cg6pca.1, cg6pca.2a, cg6pca.2b and cg6pcb which were classified into g6pca and g6pcb subtypes, respectively. Evolutionary analysis revealed that cg6pca.2a and cg6pca.2b have a closer evolutionary relationship, and the same subtype members have higher homology among different species. A classical PAP2-glucose phosphates domain is found in four genes and were highly conserved. The expression patterns revealed that only cg6pca.2a elevated significantly after 12 and 24 h of both starvation and cold treatment (p < 0.05).ConclusionsThis study performed a comprehensive analysis of G6PC gene family in common carp. Moreover, cg6pca.2 may be the major functional gene in cold and fasting stress. And the transfactors, PLAG1 and Sox8, may be concerned with expression regulation of cg6pca.2.

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Genome-wide analysis reveals the spatiotemporal expression patterns of SOS3 genes in the maize B73 genome in response to salt stress

BMC Genomics ◽

10.1186/s12864-021-08287-6 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Yunying Cao ◽

Tingyu Shan ◽

Hui Fang ◽

Kangtai Sun ◽

Wen Shi ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Signal Transduction Pathway ◽

Vital Role ◽

Growth And Yield ◽

Genome Wide ◽

Close Relationship ◽

Stress Signals ◽

Group Sharing

Abstract Background Salt damage is an important abiotic stress that affects the growth and yield of maize worldwide. As an important member of the salt overly sensitive (SOS) signal transduction pathway, the SOS3 gene family participates in the transmission of stress signals and plays a vital role in improving the salt tolerance of plants. Results In this study, we identified 59 SOS3 genes in the maize B73 genome using bioinformatics methods and genome-wide analyses. SOS3 proteins were divided into 5 different subfamilies according to the phylogenetic relationships. A close relationship between the phylogenetic classification and intron mode was observed, with most SOS3 genes in the same group sharing common motifs and similar exon-intron structures in the corresponding genes. These genes were unequally distributed on five chromosomes of B73. A total of six SOS3 genes were identified as repeated genes, and 12 pairs of genes were proven to be segmentally duplicated genes, indicating that gene duplication may play an important role in the expansion of the SOS3 gene family. The expression analysis of 10 genes that were randomly selected from different subgroups suggested that all 10 genes were significantly differentially expressed within 48 h after salt treatment, of which eight SOS3 genes showed a significant decline while Zm00001d025938 and Zm00001d049665 did not. By observing the subcellular localization results, we found that most genes were expressed in chloroplasts while some genes were expressed in the cell membrane and nucleus. Conclusions Our study provides valuable information for elucidating the evolutionary relationship and functional characteristics of the SOS3 gene family and lays the foundation for further study of the SOS3 gene family in the maize B73 genome.

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Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Biomolecules ◽

10.3390/biom9050188 ◽

2019 ◽

Vol 9 (5) ◽

pp. 188 ◽

Cited By ~ 9

Author(s):

Weilong Kong ◽

Ziyun Gong ◽

Hua Zhong ◽

Yue Zhang ◽

Gangqing Zhao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Plant Cell ◽

Plant Cell Wall ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Oryza Rufipogon ◽

Potential Candidate ◽

Evolutionary Patterns

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

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Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

International Journal of Genomics ◽

10.1155/2019/7241096 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Luzhao Pan ◽

Jiaqiu Zheng ◽

Jia Liu ◽

Jun Guo ◽

Fawan Liu ◽

...

Keyword(s):

Gene Family ◽

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Pepper Plant ◽

Rna Seq ◽

Qrt Pcr ◽

Group I

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

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Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency

Genes ◽

10.3390/genes10060473 ◽

2019 ◽

Vol 10 (6) ◽

pp. 473 ◽

Cited By ~ 2

Author(s):

Duan ◽

Wang ◽

Chao ◽

Zhang ◽

Zhang

Keyword(s):

Gene Family ◽

Phylogenetic Relationships ◽

Upland Cotton ◽

Tandem Duplication ◽

Expression Profiles ◽

Expression Patterns ◽

Class Iii ◽

P Deficiency ◽

Duplication Events ◽

Class Iii Peroxidases

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

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Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.)

International Journal of Molecular Sciences ◽

10.3390/ijms221910722 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10722

Author(s):

Lu Lu ◽

Quancan Hou ◽

Linlin Wang ◽

Tianye Zhang ◽

Wei Zhao ◽

...

Keyword(s):

Zea Mays ◽

Gene Family ◽

Zea Mays L ◽

Developmental Stages ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Functional Characterization ◽

Evolutionary Relationship ◽

Segmental Duplications

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

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New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

BMC Genomics ◽

10.1186/s12864-020-07264-9 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Weihua Su ◽

Yongjuan Ren ◽

Dongjiao Wang ◽

Long Huang ◽

Xueqin Fu ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Quantitative Polymerase Chain Reaction ◽

Functional Divergence ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Functional Study ◽

Last Common Ancestor ◽

Duplicated Genes ◽

Duplication Events

Abstract Background Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Results In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections. Conclusions In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane.

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