scholarly journals Genome-Wide Identification and Characterization of the Cystatin Gene Family in Bread Wheat (Triticum aestivum L.)

2021 ◽  
Vol 22 (19) ◽  
pp. 10264
Author(s):  
Long He ◽  
Xuan Chen ◽  
Miaoze Xu ◽  
Tingting Liu ◽  
Tianye Zhang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Codon Usage ◽  
Triticum Aestivum L ◽  
Defense Responses ◽  
Codon Usage Pattern ◽  
Segmental Duplications ◽  
Wheat Evolution ◽  
Mutation Pressure ◽  
Peptide Motifs ◽  
Duplication Events

Cystatins, as reversible inhibitors of papain-like and legumain proteases, have been identified in several plant species. Although the cystatin family plays crucial roles in plant development and defense responses to various stresses, this family in wheat (Triticum aestivum L.) is still poorly understood. In this study, 55 wheat cystatins (TaCystatins) were identified. All TaCystatins were divided into three groups and both the conserved gene structures and peptide motifs were relatively conserved within each group. Homoeolog analysis suggested that both homoeolog retention percentage and gene duplications contributed to the abundance of the TaCystatin family. Analysis of duplication events confirmed that segmental duplications played an important role in the duplication patterns. The results of codon usage pattern analysis showed that TaCystatins had evident codon usage bias, which was mainly affected by mutation pressure. TaCystatins may be regulated by cis-acting elements, especially abscisic acid and methyl jasmonate responsive elements. In addition, the expression of all selected TaCystatins was significantly changed following viral infection and cold stress, suggesting potential roles in response to biotic and abiotic challenges. Overall, our work provides new insights into TaCystatins during wheat evolution and will help further research to decipher the roles of TaCystatins under diverse stress conditions.

scholarly journals Transcriptome mechanisms underlying interaction of polystyrene nanoplastics and wheat Triticum aestivum L.

2020 ◽  
Author(s):  
Qixing Zhou ◽  
Jiapan Lian ◽  
Weitao Liu ◽  
Shuzhen Men ◽  
Jiani Wu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Molecular Mechanisms ◽  
Gene Expression Pattern ◽  
Terrestrial Ecosystems ◽  
Triticum Aestivum L ◽  
Defense Responses ◽  
Mapk Signaling ◽  
Crop Plants ◽  
Plant Performance ◽  
Network Analyses

Abstract Microplastics (MPs) and nanoplastics (NPs) have inevitably entered and accumulated in terrestrial ecosystems. Recently, the report on MPs/NPs taken-up by crop plants has raised particular concerns. However, molecular mechanisms underlying the interaction of MPs/NPs and crop plant are still vague and elusive. To address this scientific gap, we identified differentially expressed genes (DEGs) and performed co-expression network analyses in hydroponically grown wheat (Triticum aestivum L.) with ambient polystyrene NPs (PSNPs) concentration (0-10 mg/L). PSNPs could significantly shape the gene expression pattern in wheat with a tissue-specific mode. Four regulatory modules associated with the plant performance and nutrient capture were identified using WGCNA analysis. In addition, carbon metabolism, amino acid biosynthesis, MAPK signaling pathway-plant, plant hormone signal transduction, and plant-pathogen interaction were the most enriched KEGG pathways for all DEGs and target module eigengenes. These results confirm that NPs-induced genetic changes are the dominating driven forces for the observed plant growth or defense responses, shedding new light on the molecular mechanism and environmental implication behind the interaction of NPs and crop plants.

scholarly journals Comprehensive analysis of polygalacturonase family highlights candidate genes related to pollen development and male fertility in wheat (Triticum aestivum L.)

2019 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Zhiquan Yang ◽  
Wei Li ◽  
Qi Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Candidate Genes ◽  
Pollen Development ◽  
Male Fertility ◽  
Triticum Aestivum L ◽  
Segmental Duplications ◽  
Rna Seq ◽  
Male Sterile ◽  
Wide Range

Abstract Background: Polygalacturonase (PG) belongs to a large family of hydrolases with important functions in cell separation during plant growth and development via the degradation of pectin. The specific expression of PG genes in anthers may be significant for male sterility research and hybrid wheat breeding, but it has not been characterized in wheat (Triticum aestivum L.). Results: We systematically studied the PG gene family using the latest published wheat reference genomic information. In total, 113 wheat PG genes were identified and renamed as TaPG01–113 based on their chromosomal positions. The PG genes are unequally distributed on 21 chromosomes and classified according to six categories from A–F. Analysis of the gene structures and conserved motifs demonstrated that the Class C and D TaPGs have relatively short gene sequences and a small number of introns. Class E TaPGs are the least conserved and lack conserved domain III. Polyploidy and segmental duplications in wheat were mainly responsible for the expansion of the wheat PG gene family. Predictions of cis-elements indicate that TaPGs have a wide range of functions, including the responses to light, hypothermia, anaerobic conditions, and hormonal stimulation, as well as being involved in meristematic tissue expression. RNA-seq showed that TaPGs have specific temporal and spatial expression characteristics. Twelve spike-specific TaPGs were screened using RNA-seq data and verified by qRT-PCR in the sterile and fertile anthers of thermo-sensitive male-sterile wheat. Four important candidate genes were identified as involved in the male fertility determination process. In fertile anthers, TaPG09 may be involved in the separation of pollen. TaPG87 and TaPG95 could play important roles in anther dehiscence. TaPG93 may be related to pollen development and pollen tube elongation. Conclusions: We analyzed the wheat PG gene family and identified four important TaPGs with differential expression levels in the wheat fertility conversion process. Our findings may facilitate functional investigations of the wheat PG gene family and provide new insights into the fertility conversion mechanism in male-sterile wheat.

scholarly journals Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 991
Author(s):  
Huiguang Wu ◽  
Zhengyu Bao ◽  
Chunxiao Mou ◽  
Zhenhai Chen ◽  
Jingwen Zhao
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Similarity Index ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Broad Host Range ◽  
Mutation Pressure ◽  
Porcine Astrovirus ◽  
Usage Patterns

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

scholarly journals Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

2018 ◽  
Vol 19 (12) ◽  
pp. 4010
Author(s):  
Zhaocai Li ◽  
Wen Hu ◽  
Xiaoan Cao ◽  
Ping Liu ◽  
Youjun Shang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Family Members ◽  
Synonymous Codon Usage ◽  
Amino Acid Usage ◽  
Codon Usage Pattern ◽  
Evolutionary Trend ◽  
Mutation Pressure ◽  
Wide Range

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

scholarly journals Codon Usage Bias in Two Hemipteran Insect Species: Bemisia tabaci and Homalodisca coagulata

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Jyotika Sharma ◽  
Supriyo Chakraborty ◽  
Arif Uddin
Keyword(s):  
Codon Usage ◽  
Bemisia Tabaci ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Insect Species ◽  
Codon Usage Pattern ◽  
Mutation Pressure ◽  
Homalodisca Coagulata ◽  
Highly Expressed Genes ◽  
Hemipteran Insect

Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species.

MicroRNA regulated defense responses in Triticum aestivum L. during Puccinia graminis f.sp. tritici infection

2011 ◽  
Vol 39 (2) ◽  
pp. 817-824 ◽  
Author(s):  
Om Prakash Gupta ◽  
Vipin Permar ◽  
Vikas Koundal ◽  
Uday Dhari Singh ◽  
Shelly Praveen
Keyword(s):  
Triticum Aestivum ◽  
Triticum Aestivum L ◽  
Defense Responses ◽  
Puccinia Graminis

scholarly journals Characterization of codon usage pattern in SARS-CoV-2

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Codon Usage Pattern ◽  
Slight Variation ◽  
Usage Pattern ◽  
Mutation Pressure ◽  
Genetic Traits ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.

scholarly journals Characterization of Codon Usage Pattern in SARS-CoV-2

2020 ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Codon Usage Pattern ◽  
Slight Variation ◽  
Usage Pattern ◽  
Mutation Pressure ◽  
Genetic Traits ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.

scholarly journals Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

2020 ◽  
Author(s):  
Saif M. Khodary ◽  
Ali Mostafa Anwar
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Homo Sapiens ◽  
World Health ◽  
Codon Usage Pattern ◽  
Design Strategies ◽  
Mutation Pressure ◽  
A Genome ◽  
The World

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens. Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.

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