scholarly journals Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

2020 ◽  
Author(s):  
Hongwei Zhang ◽  
Xinxia Liang ◽  
Shuo Zhou ◽  
Haibo Wang
Keyword(s):  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Suppressor Gene ◽  
Pcr Analysis ◽  
Genome Wide Analysis ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Mads Box Gene ◽  
And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

scholarly journals A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 396 ◽  
Author(s):  
Trine B Rounge ◽  
Thomas Rohrlack ◽  
Alexander J Nederbragt ◽  
Tom Kristensen ◽  
Kjetill S Jakobsen
Keyword(s):  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nonribosomal Peptide ◽  
Genome Wide Analysis ◽  
Planktothrix Rubescens ◽  
Genome Wide ◽  
A Genome ◽  
Peptide Synthetase

Genome-wide Analysis of the Distribution of Riboswitches and Function Analyses of the Corresponding Downstream Genes in Prokaryotes

2018 ◽  
Vol 14 (1) ◽  
pp. 53-61
Author(s):  
Xinfeng Li ◽  
Fang Chen ◽  
Jinfeng Xiao ◽  
Shan-Ho Chou ◽  
Xuming Li ◽  
...  
Keyword(s):  
Functional Categories ◽  
Gene Expressions ◽  
Context Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Genome Context Analysis ◽  
Genome Context ◽  
And Function

Background: Riboswitches are structured elements that usually reside in the noncoding regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene expressions. To date, more than twenty different classes of riboswitches have been characterized to sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal ions, etc. </P><P> Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and function analyses of the corresponding downstream genes in prokaryotes. Results: In this study, we have completed a genome context analysis of 27 riboswitches to elucidate their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079 prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was applied to predict and classify the possible functions of corresponding downstream genes of these riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG functional categories, in which the two main clusters &quot;coenzyme metabolism [H]&quot; and &quot;amino acid transport and metabolism [E]&quot; were the most significantly enriched. Conclusion: Riboswitches are found to be widespread in bacteria, among which three main classes of TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of functions were associated with the corresponding downstream genes, suggesting that a wide extend of regulatory roles were mediated by these riboswitches in prokaryotes.

scholarly journals Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

2018 ◽  
Vol 19 (9) ◽  
pp. 2478 ◽  
Author(s):  
Qinglong Dong ◽  
Dingyue Duan ◽  
Shuang Zhao ◽  
Bingyao Xu ◽  
Jiawei Luo ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Sequence Alignments ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

scholarly journals Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico

2019 ◽  
Author(s):  
Takahiro Nakamura ◽  
Muhamad Fahmi ◽  
Jun Tanaka ◽  
Kaito Seki ◽  
Yukihiro Kubota ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Glycoside Hydrolases ◽  
Data Driven ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Class 1 ◽  
And Function ◽  
Multicellular Organisms ◽  
Disordered Regions

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy, and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3), and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.

scholarly journals The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11371
Author(s):  
Hongzhan Liu ◽  
Chaoqiong Li ◽  
Lin Qiao ◽  
Lizong Hu ◽  
Xueqin Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Tolerance ◽  
Expression Profiles ◽  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Sugar Transporter ◽  
Wheat Seedlings ◽  
Transporter Family ◽  
Genome Wide

The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.

scholarly journals A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4

2021 ◽  
Vol 37 (4) ◽  
pp. 389-395
Author(s):  
Da-Ran Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Bacterial Species ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Plant Diseases ◽  
Local Alignment ◽  
Plant Tissues ◽  
Biosynthetic Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.

scholarly journals Genome-Wide Identification and Analysis of HAK/KUP/KT Potassium Transporters Gene Family in Wheat (Triticum aestivum L.)

2018 ◽  
Vol 19 (12) ◽  
pp. 3969 ◽  
Author(s):  
Xiyong Cheng ◽  
Xiaodan Liu ◽  
Weiwei Mao ◽  
Xurui Zhang ◽  
Shulin Chen ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Chromosomal Distribution ◽  
Wheat Seedlings ◽  
Expression Levels ◽  
Transporter Family ◽  
Genome Wide ◽  
A Genome ◽  
Potassium Transporters

In plants, the HAK (high-affinity K+)/KUP (K+ uptake)/KT (K+ transporter) family represents a large group of potassium transporters that play important roles in plant growth and environmental adaptation. Although HAK/KUP/KT genes have been extensively investigated in many plant species, they remain uncharacterized in wheat, especially those involved in the response to environmental stresses. In this study, 56 wheat HAK/KUP/KT (hereafter called TaHAKs) genes were identified by a genome-wide search using recently released wheat genomic data. Phylogenetic analysis grouped these genes into four clusters (Ι, II, III, IV), containing 22, 19, 7 and 8 genes, respectively. Chromosomal distribution, gene structure, and conserved motif analyses of the 56 TaHAK genes were subsequently performed. In silico RNA-seq data analysis revealed that TaHAKs from clusters II and III are constitutively expressed in various wheat tissues, while most genes from clusters I and IV have very low expression levels in the examined tissues at different developmental stages. qRT-PCR analysis showed that expression levels of TaHAK genes in wheat seedlings were significantly up- or downregulated when seedlings were exposed to K+ deficiency, high salinity, or dehydration. Furthermore, we functionally characterized TaHAK1b-2BL and showed that it facilitates K+ transport in yeast. Collectively, these results provide valuable information for further functional studies of TaHAKs, and contribute to a better understanding of the molecular basis of wheat development and stress tolerance.

scholarly journals Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico

2019 ◽  
Vol 20 (24) ◽  
pp. 6290 ◽  
Author(s):  
Takahiro Nakamura ◽  
Muhamad Fahmi ◽  
Jun Tanaka ◽  
Kaito Seki ◽  
Yukihiro Kubota ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Glycoside Hydrolases ◽  
Data Driven ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Class 1 ◽  
And Function ◽  
Multicellular Organisms ◽  
Disordered Regions

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.

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