scholarly journals Genome-wide Identification of the POD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera L)

2019 ◽  
Author(s):  
Huilin Xiao ◽  
Chaoping Wang ◽  
Nadeem Khan ◽  
Mengxia Chen ◽  
Weihong Fu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Sequence Data ◽  
Expression Patterns ◽  
Critical Role ◽  
Chromosomal Mapping ◽  
Integrated Analysis ◽  
Vitis Vinifera L ◽  
Specific Response ◽  
Evolutionary Analysis ◽  
Gene Pairs

Abstract The purpose of this study is by extending the analysis of class III peroxidases (PODs) in grapevine and provide further insights into the organ-specific developmental role in transcriptional dynamics and gene duplication analysis of this economically important fruit crop species. Herein, we comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine. In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

scholarly journals Genome-wide Identification of the Class III POD Gene Family and their Expression Profiling in Grapevine (Vitisvinifera L)

2020 ◽  
Author(s):  
Huilin Xiao ◽  
Chaoping Wang ◽  
Nadeem Khan ◽  
Mengxia Chen ◽  
Weihong Fu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Critical Role ◽  
Chromosomal Mapping ◽  
Integrated Analysis ◽  
Specific Response ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Gene Pairs ◽  
Genome Wide

Abstract Background : The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date. Results : We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine. Conclusions : In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

scholarly journals Genome-Wide Identification, Evolution, and Transcriptional Profiling ofPP2CGene Family inBrassica rapa

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Nadeem Khan ◽  
Han Ke ◽  
Chun-mei Hu ◽  
Emal Naseri ◽  
Muhammad Salman Haider ◽  
...  
Keyword(s):  
Sequence Data ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Vital Role ◽  
Future Research ◽  
Evolutionary Analysis ◽  
Paralogous Gene ◽  
Gene Pairs ◽  
Genome Wide

The type 2C protein which belongs to the major group of protein phosphatases (PP2C) plays a vital role in abscisic acid (ABA) signaling and signal transductions processes. In the present study, 131PP2Cgenes were identified in total inBrassica rapaand categorized into thirteen subgroups based on their phylogenetic relationships. TheseB. rapaPP2C are structurally conserved based on amino acid sequence alignment, phylogenetic analysis, and conserved domains. Moreover, we utilized previously reported RNA-sequence data on various tissues (root, stem, leaf, flower, and silique), which suggests overlapping expression pattern in 29 paralogous gene pairs. The qRT-PCR validation of 15 paralogous gene pairs depicts distinct expression patterns in response to various abiotic stresses, such as heat, cold, ABA, and drought. Interestingly, stress-responsiveBraPP2Ccandidate genes were also identified, suggesting their significance in stress-tolerance mechanism inB. rapa. The evolutionary analysis for 15 paralogous gene pairs suggested that only three pairs have the positive selection and remaining were purifying in nature. The presented results of this study hasten our understanding of the molecular evolution of thePP2Cgene family inB. rapa. Thus, it will be ultimately helping in future research for facilitating the functional characterization ofBraPP2Cgenes in developing the abiotic stress tolerant plants.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

scholarly journals Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L.

2019 ◽  
Vol 20 (6) ◽  
pp. 1395 ◽  
Author(s):  
Hamna Shazadee ◽  
Nadeem Khan ◽  
Jingjing Wang ◽  
Chencan Wang ◽  
Jianguo Zeng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Profiling ◽  
Critical Role ◽  
Fiber Development ◽  
Chromosomal Mapping ◽  
Composition Analysis ◽  
Specific Gene ◽  
Specific Response ◽  
Pp2c Gene

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.

scholarly journals Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

2020 ◽  
Vol 2020 ◽  
pp. 1-19
Author(s):  
Chenyang Liu ◽  
Dongliang Yuan ◽  
Tong Liu ◽  
Mengge Xing ◽  
Wenying Xu ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Cultivated Species ◽  
Arachis Duranensis ◽  
Gene Structures ◽  
Wild Peanut

RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.

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

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.

scholarly journals Single-cell analysis of microglial transcriptomic diversity in subarachnoid hemorrhage

2021 ◽  
Author(s):  
Junfan CHEN ◽  
Lei SUN ◽  
Hao LYU ◽  
Zhiyuan ZHENG ◽  
Huasheng LAI ◽  
...  
Keyword(s):  
Subarachnoid Hemorrhage ◽  
Single Cell ◽  
Expression Patterns ◽  
Critical Role ◽  
Marker Gene ◽  
Transcriptional Analysis ◽  
Integrated Analysis ◽  
Cellular Interactions ◽  
Monitoring Methods ◽  
Gene Markers

Background: Subarachnoid hemorrhage (SAH) is a severe stroke and the advanced treatment for SAH is still limited. Recent studies have shown that microglia-mediated neuroinflammation plays a critical role in the pathogenesis of SAH. Microglia can transform their states in response to central nervous system injury. However, the transcriptomic features of microglia remained unknown in SAH. Recent developed single-cell RNA sequencing (scRNA-seq) provides a possible way to solve this problem. Methods: Endovascular perforation (EVP) murine SAH model was established to reproduce experimental SAH. Microglia states are examined with immune staining and quantitate analysis. Post-SAH microglial single-cell suspension were harvest and sequenced using 10X scRNA-seq platform. Then, the detailed single-cell transcriptomic characterization of post-SAH microglia were analyzed with bioinformatics. Results: Transcriptional analysis revealed at least ten diverse microglial subgroups, including SAH-associated microglia (SAM), inflammatory-associated microglia (IAM) and proliferation-associated microglia (PAM), which all exhibit distinct marker gene expression patterns. Microglia subsets interaction reveals the functional relationship between elevated signaling pathways and microglial sub-populations in SAH. Receptor-ligand pair analysis revealed that complex inter-cellular interactions exist between the microglia subsets and other cell types, and indicated that microglia are important mediators of neuroinflammation after SAH. Integrated analysis with normal microglia further proved the existence of these microglia subpopulations and different gene markers associated with SAH were clarified. Conclusions: Collectively, we first report the single-cell transcriptome of post-SAH microglia and found specific biomarkers related to the neuroinflammation in SAH. These results enhanced our understanding of the pathological mechanisms of microglial response to SAH, and may guide future development of SAH monitoring methods and therapeutics.

scholarly journals Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)

2019 ◽  
Vol 20 (13) ◽  
pp. 3180 ◽  
Author(s):  
Nadeem Khan ◽  
Fizza Fatima ◽  
Muhammad Salman Haider ◽  
Hamna Shazadee ◽  
Zhongjie Liu ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Vitis Vinifera L ◽  
Specific Response ◽  
Gene Duplications ◽  
Crop Species ◽  
Specific Expression ◽  
Tissue Specific

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.

scholarly journals Comparative profiling of microRNA expression in the developing seeds of high- and low-oil tea oil camellia (Camellia oleifera) cultivars

2019 ◽  
Author(s):  
Bo Wu ◽  
Chengjiang Ruan ◽  
Wanchen Zhang ◽  
Asad Hussain Shah ◽  
Sihei Liu
Keyword(s):  
Lipid Metabolism ◽  
Target Genes ◽  
Sequence Data ◽  
Southern China ◽  
Expression Patterns ◽  
Integrated Analysis ◽  
Small Rna Sequencing ◽  
Camellia Oleifera ◽  
Illumina Platform ◽  
Function Modules

Abstract Background Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal values and has been widely planted in southern China. However, there are few reports on the identification of miRNAs involved in seed lipid metabolism in high- and low-oil cultivars of tea oil camellia. Results An miRNA sequencing database was constructed for an Illumina platform, which was used to perform high-throughput small RNA sequencing of seeds of high- and low-oil cultivars of tea oil camellia at four different developmental stages, and the important relevant miRNAs and their target genes were identified. A total of 196 miRNAs, including 156 known miRNAs from 35 families and 40 novel miRNAs, were identified, and 55 significantly differentially expressed miRNAs were found. An integrated analysis of miRNA and mRNA transcriptome sequence data and qRT-PCR-based information was performed and revealed that 10 miRNA-mRNA function modules were related to lipid metabolism and 23 miRNA-mRNA function modules were involved in the regulation of seed size. Conclusion Mining and studying the expression patterns and functions of miRNAs and their regulatory target genes can not only promote the development of miRNAs related to tea oil camellia in public resource databases but also provide important theoretical value and a scientific basis for the genetic improvement of new varieties of tea oil camellia in the future.

scholarly journals Identification and expression analysis of Tubulin gene family in upland cotton

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Baojun CHEN ◽  
Junjie ZHAO ◽  
Guoyong FU ◽  
Xinxin PEI ◽  
Zhaoe PAN ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Critical Role ◽  
Fiber Development ◽  
Pcr Analysis ◽  
Evolutionary Analysis ◽  
Tubulin Gene ◽  
Core Element ◽  
Protein Motifs ◽  
Seed Epidermis

Abstract Background Cotton fibers are single-celled extensions of the seed epidermis, a model tissue for studying cytoskeleton. Tubulin genes play a critical role in synthesizing the microtubules (MT) as a core element of the cytoskeleton. However, there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton. Therefore, the identification and portrayal of G. hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding. Result In this study, we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G. hirsutum. Phylogenetic analysis showed that tubulin family genes were classified into three subfamilies. The protein motifs and gene structure of α-, β-tubulin genes are more conserved compared with γ-tubulin genes. Most tubulin genes are located at the proximate ends of the chromosomes. Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12 α-tubulin and 7 β-tubulin genes are specifically expressed during different fiber development stages. However, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 had differential expression patterns at distinct stages of fiber development in varieties J02508 and ZRI015. Conclusion In this study, the evolutionary analysis showed that the tubulin genes were divided into three clades. The genetic structures and molecular functions were highly conserved in different plants. Three candidate genes, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength.

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