Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum

2019 ◽  
Vol 61 (3) ◽  
pp. 616-630 ◽  
Author(s):  
Zhen Li ◽  
Xiuting Hua ◽  
Weiming Zhong ◽  
Yuan Yuan ◽  
Yongjun Wang ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Diploid Species ◽  
Amino Acid Sequences ◽  
Segmental Duplications ◽  
Saccharum Spontaneum ◽  
Expression Profile Analysis ◽  
Gene Structures ◽  
Conserved Gene

Abstract WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs’ expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs’ expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.

scholarly journals Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum)

Plants ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 52 ◽  
Author(s):  
Jun Cao ◽  
Xiaona Tan
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Functional Studies ◽  
Gene Structures ◽  
Functional Relevance ◽  
Conserved Gene ◽  
Chitinase Genes

Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

scholarly journals Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum)

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Dongdong Zhang ◽  
Sujuan Gao ◽  
Ping Yang ◽  
Jie Yang ◽  
Songguang Yang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solanum Lycopersicum ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Nucleosome Position ◽  
Fruit Fly ◽  
Amino Acid Residues ◽  
Expression Profile Analysis ◽  
Wide Range ◽  
Chromatin Remodeling Complexes

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

scholarly journals Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9131
Author(s):  
Jie Cui ◽  
Xinyan Li ◽  
Junliang Li ◽  
Congyu Wang ◽  
Dayou Cheng ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Salinity Stress ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Plant Growth And Development ◽  
Auxin Response ◽  
Expression Profile Analysis ◽  
Sequence Identification ◽  
Genome Wide ◽  
Intron Structure

Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.

Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in Teak (Tectona Grandis)

2020 ◽  
Author(s):  
Xi-Yang Wang ◽  
Jie Song ◽  
Jia-Hui Xing ◽  
Jun-Feng Liang ◽  
Bi-ying Ke
Keyword(s):  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Large Family ◽  
Tectona Grandis ◽  
Duplication Event ◽  
Whole Genome Sequence ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: WRKY proteins comprise a large family of transcription factors that play vital roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in teak (Tectona grandis). The recent release of the whole-genome sequence of teak allowed us to perform a genome-wide investigation into the organization and expression profiling of teak WRKY genes. Results: In the present study, 102 teak WRKY (TgWRKY) genes were identified and renamed as per their positions on chromosome and scaffolds. According to their structural and phylogenetic analysis, the 102 TgWRKYs were further classified into three main groups with seceral subgroups. The segmental duplication event played a major role in the expansion of teak WRKY gene family and three WGD events were inferred. Expression profiles derived from transcriptome data exhibited distinct expression patterns of TgWRKY genes in various tissues and inresponse to different abiotic stress.Conclusions: 102 TgWRKY genes were identified in teak and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This study generated an important resource that will provide helpful information for further exploration of the TgWRKY genes role in the regulatory mechanism in response to abiotic stresses.

Conserved gene structures and expression signals in methanogenic archaebacteria

1989 ◽  
Vol 35 (1) ◽  
pp. 52-57 ◽  
Author(s):  
Rudolf Allmansberger ◽  
Martin Bokranz ◽  
Lothar Kröckel ◽  
Jürgen Schallenberg ◽  
Albrecht Klein
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Structural Genes ◽  
Promoter Sequences ◽  
Ribosome Binding Sites ◽  
Homologous Genes ◽  
Gene Structures ◽  
Conserved Gene

A comparative analysis of cotranscribed gene clusters comprising the structural genes mcrA, mcrB, mcrC, mcrD, and mcrG was carried out in three species of methanogens. mcrA, mcrB, and mcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of the mcr gene products among different species of methanogens varies. No correlation was found between the conservation of the G + C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes of Methanobacterium thermoautotrophicum as evolutionary markers with their equivalents in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster showed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of the mcr genes.Key words: archaebacteria, methanogens, gene structure, RNA polymerase, promoter.

scholarly journals Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon

2008 ◽  
Vol 105 (40) ◽  
pp. 15493-15498 ◽  
Author(s):  
Melanie H. Kucherlapati ◽  
Kan Yang ◽  
Kunhua Fan ◽  
Mari Kuraguchi ◽  
Dmitriy Sonkin ◽  
...  
Keyword(s):  
Small Intestine ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tumor Location ◽  
Proximal Colon ◽  
Gi Tract ◽  
Expression Profile Analysis ◽  
Tumor Types

To examine the role of Rb1 in gastrointestinal (GI) tumors, we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villin-cre transgene (RBVCA). These animals had exon 19 deleted from Rb1 throughout the GI tract. We have shown previously that Rb1 deficiency is insufficient for GI tumor initiation, with inactivation of an Apc allele capable of overcoming the insufficiency. In this study we demonstrate that RBVCA mice have reduced median survival because of an increase in tumor incidence and multiplicity in the cecum and the proximal colon. Large intestinal tumors are predominantly adenomas, whereas the tumors of the small intestine are a mixture of adenomas and adenocarcinomas. We find truncation mutations to the second Apc allele in tumors of both the large and small intestine. Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. Substantial expression patterns compare to human colorectal cancer, including recapitulation of embryonic genes. Our results indicate that Rb1 has significant influence over tumor location in the GI tract, and that both cecal and duodenal tumors initiate through inactivation of Apc. Expression profile analysis indicates the two tumor types differentially regulate distinct sets of genes that are over-expressed in a majority of human colorectal carcinomas.

scholarly journals Systematic Analysis of the bZIP Family in Tobacco and Functional Characterization of NtbZIP62 Involvement in Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 148
Author(s):  
Zhiyuan Li ◽  
Jiangtao Chao ◽  
Xiaoxu Li ◽  
Gongbo Li ◽  
Dean Song ◽  
...  
Keyword(s):  
Salt Stress ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Segmental Duplications ◽  
Basic Leucine Zipper ◽  
Systematic Analysis ◽  
Duplication Events ◽  
Tobacco Genome ◽  
Gene Structures

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in the tobacco genome were classified into 11 groups with Arabidopsis and tomato bZIP members, based on the results of a phylogenetic analysis. An examination of gene structures and conserved motifs revealed relatively conserved exon/intron structures and motif organization within each group. The results of an investigation of whole-genome duplication events indicated that segmental duplications were crucial for the expansion of the bZIP gene family in tobacco. Expression profiles confirmed that the NtbZIP genes are differentially expressed in various tissues, and several genes are responsive to diverse stresses. Notably, NtbZIP62, which was identified as an AtbZIP37/ABF3 homolog, was highly expressed in response to salinity. Subcellular localization analyses proved that NtbZIP62 is a nuclear protein. Furthermore, the overexpression of NtbZIP62 in tobacco significantly enhanced the salt stress tolerance of the transgenic plants. The results of this study may be relevant for future functional analyses of the bZIP genes in tobacco.

scholarly journals Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

2021 ◽  
Vol 22 (4) ◽  
pp. 2026
Author(s):  
Weiye Peng ◽  
Wei Li ◽  
Na Song ◽  
Zejun Tang ◽  
Jing Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profile ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Brachypodium Distachyon ◽  
Defense Responses ◽  
Regulatory Elements ◽  
Blast Disease ◽  
Expression Profile Analysis ◽  
Genome Wide

The GATA proteins, functioning as transcription factors (TFs), are involved in multiple plant physiological and biochemical processes. In this study, 28 GATA TFs of Brachypodium distachyon (BdGATA) were systematically characterized via whole-genome analysis. BdGATA genes unevenly distribute on five chromosomes of B. distachyon and undergo purifying selection during the evolution process. The putative cis-acting regulatory elements and gene interaction network of BdGATA were found to be associated with hormones and defense responses. Noticeably, the expression profiles measured by quantitative real-time PCR indicated that BdGATA genes were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatment, and 10 of them responded to invasion of the fungal pathogen Magnaporthe oryzae, which causes rice blast disease. Genome-wide characterization, evolution, and expression profile analysis of BdGATA genes can open new avenues for uncovering the functions of the GATA genes family in plants and further improve the knowledge of cellular signaling in plant defense.

scholarly journals Genomic Survey, Characterization, and Expression Profile Analysis of the SBP Genes in Pineapple (Ananas comosus L.)

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Hina Ali ◽  
Yanhui Liu ◽  
Syed Muhammad Azam ◽  
Zia ur Rahman ◽  
S. V. G. N. Priyadarshani ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Ananas Comosus ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Expression Profile Analysis ◽  
Expression Studies ◽  
Flower And Fruit Development ◽  
Regulatory Functions

Gene expression is regulated by transcription factors, which play many significant developmental processes. SQUAMOSA promoter-binding proteins (SBP) perform a variety of regulatory functions in leaf, flower, and fruit development, plant architecture, and sporogenesis. 16 SBP genes were identified in pineapple and were divided into four groups on basis of phylogenetic analysis. Five paralogs in pineapple for SBP genes were identified with Ka/Ks ratio varied from 0.20 for AcSBP14 and AcSBP15 to 0.36 for AcSBP6 and AcSBP16, respectively. 16 SBP genes were located on 12 chromosomes out of 25 pineapple chromosomes with highly conserved protein sequence structures. The isoionic points of SBP ranged from 6.05 to 9.57, while molecular weight varied from 22.7 to 121.9 kD. Expression profiles of SBP genes revealed that AcSBP7 and AcSBP15 (leaf), AcSBP13, AcSBP12, AcSBP8, AcSBP16, AcSBP9, and AcSBP11 (sepal), AcSBP6, AcSBP4, and AcSBP10 (stamen), AcSBP14, AcSBP1, and AcSBP5 (fruit) while the rest of genes showed low expression in studied tissues. Four genes, that is, AcSBP11, AcSBP6, AcSBP4, and AcSBP12, were highly expressed at 4°C, while AcSBP16 were upregulated at 45°C. RNA-Seq was validated through qRT-PCR for some genes. Salt stress-induced expression of two genes, that is, AcSBP7 and AcSBP14, while in drought stress, AcSBP12 and AcSBP15 were highly expressed. Our study lays a foundation for further gene function and expression studies of SBP genes in pineapple.

Sign in / Sign up

Export Citation Format

Share Document