scholarly journals Genome-wide identification of MscS like gene family in Cicer arietinum using bioinformatics approach

2018 ◽  
Vol 7 (2) ◽  
pp. 2002 ◽  
Author(s):  
Noymi Basumatary ◽  
Archana Kumari ◽  
Jatin Sarmah
Keyword(s):  
Subcellular Localization ◽  
Gene Family ◽  
Cicer Arietinum ◽  
Genome Structure ◽  
Evolutionary Relationship ◽  
Chemical Properties ◽  
Gene Families ◽  
Genome Wide ◽  
Physico Chemical ◽  
Structure Annotation

In plants, the mechanosensitive channels have important roles in proprioception, gravity sensing, growth of pollen tube and controlling the shape and size of plastid. In the present study, we performed computational analysis and identified the mechanosensitive channel of small conductance like (MscS) gene family in Cicer arietinum (chickpea). Six Cicer arietinum MscS-like (CaMSL) genes were identified. These six genes were distributed on four different chromosomes. A detailed overview of CaMSL genes in Cicer arietinum is explored by using a total of 33107 proteins from chickpea. On the basis of BLAST analysis, presence of complete ORF and evolutionary relationship we identified 6 genes (named as CaMSL1, CaMSL2, CaMSL3, CaMSL4, CaMSL5 and CaMSL6). Further, the transmembrane regions, subcellular localization, physico-chemical properties, gene structure analysis and genome structure annotation of the identified genes confirmed that the identified genes might act for transmembrane proteins as well as their subcellular localization prediction demonstrated three genes to be located in the plasma membrane, two in the chloroplast membrane, one in the mitochondrion. Thus, further analysis of the data obtained from this study will help to make a baseline to increase the understanding of involvement of MSL gene families in plant growth, development and other functions in C. arietinum.

scholarly journals Genome-wide identification and expression analysis of CYP450 gene family in Cucumis sativus L.

2021 ◽  
Author(s):  
hongyu wang ◽  
Pengfei Li ◽  
Yu Wang ◽  
Chunyu Chi ◽  
Guohua Ding
Keyword(s):  
Subcellular Localization ◽  
Gene Family ◽  
Cucumis Sativus ◽  
Expression Profile ◽  
Evolutionary Relationship ◽  
Evolutionary Analysis ◽  
Cucumis Sativus L ◽  
P450 Gene ◽  
Genome Wide ◽  
A Genome

Abstract The cytochrome P450 (CYP450) gene family plays a vital role in basic metabolism and enhances plant resistance to stress and pests. However, little information is available on the genome-wide characterization and evolutionary relationship of the CYP450 gene family in Cucumis sativus L. In the present study, a genome-wide bioinformatics analysis was performed, including gene structure, conserved motif, cis-acting promoter element, evolutionary analysis, collinearity, subcellular localization, and expression profile. The gene expression profile of CYP450 was verified using transcriptome sequencing and quantitative reverse transcription polymerase chain reaction. A total of 165 P450 genes were identified in the cucumber genome. These genes were classified into eight subfamilies and unevenly distributed on seven chromosomes. Subcellular localization predicted that most of P450 genes were located in chloroplasts and a few were located on the plasma membrane. CYP450 genes were differentially expressed in different tissues and in response to salicylic acid (SA) treatment. The sizes of all cucumber P450 proteins ranged from 317 to 1,056 aa, the theoretical isoelectric points ranged from 5.05 to 10.31, and the molecular weights ranged from 36,095 to 121,403 KD. This study provides a theoretical basis for further research on the biological functions of the P450 gene in cucumber plants.

scholarly journals BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Akram Ali Baloch ◽  
Agha Muhammad Raza ◽  
Shahjahan Shabbir Ahmed Rana ◽  
Saad Ullah ◽  
Samiullah Khan ◽  
...  
Keyword(s):  
Gene Family ◽  
Pseudomonas Syringae ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Evolutionary Model ◽  
Phylogenetic Groups ◽  
Genome Wide ◽  
Physico Chemical ◽  
Gene Structures

AbstractCNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.

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

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.

scholarly journals Ectopic Expression of Virus Innexins in Heliothis virescens Disrupts Hemocyte-Mediated Encapsulation and Host Viability

2019 ◽  
Author(s):  
Peng Zhang ◽  
Matthew W Turnbull
Keyword(s):  
Gene Family ◽  
Gap Junction ◽  
Host Range ◽  
Heliothis Virescens ◽  
Genome Structure ◽  
Ectopic Expression ◽  
Recombinant Baculovirus ◽  
Gene Families ◽  
Recombinant Baculoviruses ◽  
Susceptible Host

1.AbstractPolydnaviruses are dsDNA viruses associated with endoparasitoid wasps. Delivery of the virus during parasitization of a caterpillar and subsequent virus gene expression is required for production of an amenable environment for parasitoid offspring development. Consequently, understanding of Polydnavirus gene function provides insight into mechanisms of host susceptibility and parasitoid wasp host range. Polydnavirus genes predominantly are arranged in multimember gene families, one of which is the vinnexins, which are virus homologues of insect gap junction genes, the innexins. Previous studies of Campoletis sonorensis Ichnovirus Vinnexins using various heterologous systems have suggested the four encoded members may provide different functionality in the infected caterpillar host. Here, we expressed two of the members, vnxG and vnxQ2, using recombinant baculoviruses in susceptible host, the caterpillar Heliothis virescens. Following intrahemocoelic injections, we observed >90% of hemocytes (blood cells) were infected, producing recombinant protein. Larvae infected with a vinnexin-recombinant baculovirus exhibited significantly reduced molting rates relative to larvae infected with a control recombinant baculovirus and mock infected larvae. Similarly, larvae infected with vinnexin-recombinant baculoviruses were less likely to molt relative to controls, and showed reduced ability to encapsulate chromatography beads in an immune assay. In most assays, the VnxG protein was associated with more severe pathology than VnxQ2. These results, in light of previous findings, support that Polydnavirus Vinnexin gene family members may provide complementary, rather than redundant, effects. This in turn indicates a need to test gene family member functionality across infected hosts for effects to determine member contribution to host range.2.ImportancePolydnaviruses are obligate mutualistic associates of highly speciose wasp taxa that parasitize caterpillars. Expression of Polydnavirus-encoded genes in hosts parasitized by wasps is necessary for successful parasitization, and an unusual genome structure including multiple-membered gene families is hypothesized to contribute to host manipulation. We have tested this hypothesis by in vivo expression of two members of a family of Polydnavirus homologues of Innexins, or insect gap junction proteins. Previous findings demonstrated that the two Vinnexins induce different physiological alterations in heterologous systems. Here, in host caterpillars, we observed differential alteration by the two proteins of host immune cell (hemocyte) bioelectrical physiology and the immune response of encapsulation. Not only do our data suggest a linkage between cellular bioelectricity and immunity in insects, but they support that gene family expansion has functional consequences to both Polydnavirus and host wasp success.

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

scholarly journals Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5816 ◽  
Author(s):  
Lidong Hao ◽  
Xiuli Qiao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Gene Families ◽  
Regulatory Elements ◽  
Vital Role ◽  
Signal Pathways ◽  
Cis Acting ◽  
Genome Wide ◽  
Gramineous Plant ◽  
Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3955 ◽  
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.

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

Plants ◽  
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.

scholarly journals In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Awdhesh Kumar Mishra ◽  
Jinhee Choi ◽  
Muhammad Fazle Rabbee ◽  
Kwang-Hyun Baek
Keyword(s):  
Gene Family ◽  
Abc Transporter ◽  
Abc Transporters ◽  
In Silico ◽  
Gene Families ◽  
Protein Domain ◽  
Atp Binding ◽  
Transporter Gene ◽  
Genome Wide ◽  
Atp Binding Cassette

ATP-binding cassette (ABC) transporters constitute one of the largest gene families in all living organisms, most of which mediate transport across biological membranes by hydrolyzing ATP. However, detailed studies of ABC transporter genes in the important oil crop, soybean, are still lacking. In the present study, we carried out genome-wide identification and phylogenetic and transcriptional analyses of the ABC gene family in G. max. A total of 261 G. max ABC (GmABCs) genes were identified and unevenly localized onto 20 chromosomes. Referring to protein-domain orientation and phylogeny, the GmABC family could be classified into eight (ABCA-ABCG and ABCI) subfamilies and ABCG were the most abundantly present. Further, investigation of whole genome duplication (WGD) signifies the role of segmental duplication in the expansion of the ABC transporter gene family in soybean. The Ka/Ks ratio indicates that several duplicated genes are governed by intense purifying selection during evolution. In addition, in silico expression analysis based on RNA-sequence using publicly available database revealed that ABC transporters are differentially expressed in tissues and developmental stages and in dehydration. Overall, we provide an extensive overview of the GmABC transporter gene family and it promises the primary basis for the study in development and response to dehydration tolerance.

scholarly journals Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 22 (16) ◽  
pp. 8743
Author(s):  
Mahipal Singh Kesawat ◽  
Bhagwat Singh Kherawat ◽  
Anupama Singh ◽  
Prajjal Dey ◽  
Mandakini Kabi ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Evolutionary Relationship ◽  
Triticum Aestivum L ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Homology Search ◽  
Slight Variation ◽  
Developmental Processes ◽  
Genome Wide

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.

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