scholarly journals Genome-wide phylogenetic analysis of the pathogenic potential of Vibrio furnissii

2014 ◽  
Vol 5 ◽  
Author(s):  
Thomas M. Lux ◽  
Rob Lee ◽  
John Love
Keyword(s):  
Phylogenetic Analysis ◽  
Pathogenic Potential ◽  
Genome Wide ◽  
Vibrio Furnissii

Genome-wide Identification, Phylogenetic Analysis, and Expression Profiling of CONSTANS-like (COL) Genes in Vitis vinifera

2018 ◽  
Vol 38 (2) ◽  
pp. 631-643 ◽  
Author(s):  
Ling Wang ◽  
Jingyi Xue ◽  
Weina Dai ◽  
Yujin Tang ◽  
Peijie Gong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vitis Vinifera ◽  
Expression Profiling ◽  
Genome Wide

scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1430
Author(s):  
Yuanfeng Xu ◽  
Jinbin Zheng ◽  
Yanan Yang ◽  
Zhaoxia Cui
Keyword(s):  
Phylogenetic Analysis ◽  
Environmental Stress ◽  
Tandem Duplication ◽  
High Salinity ◽  
Expression Profiles ◽  
Eriocheir Sinensis ◽  
Biological Processes ◽  
Synteny Analysis ◽  
Air Exposure ◽  
Genome Wide

DDE transposase 4 (DDE_Tnp_4) family is a large endonuclease family involved in a wide variety of biological processes. However, little information is available about this family in crustaceans. In this study, we used HMMER to identify 39 DDE_Tnp_4 family genes in Eriocheir sinensis genome, and the genes were classified into four subfamilies according to phylogenetic analysis. Gene expansions occurred among E. sinensis genome, and synteny analysis revealed that some DDE_Tnp_4 family genes were caused by tandem duplication. In addition, the expression profiles of DDE_Tnp_4 family genes in E. sinensis indicated that subfamily I and II genes were up-regulated in response to acute high salinity and air exposure stress. E. sinensis is a kind of economical crustacean with strong tolerance to environmental stress. We confirmed the expansion of DDE_Tnp_4 family genes in E. sinensis and speculated that this expansion is associated with strong tolerance of E. sinensis. This study sheds light on characterizations and expression profiles of DDE_Tnp_4 family genes in E. sinensis and provides an integrated framework for further investigation on environmental adaptive functions of DDE_Tnp_4 family in crustaceans.

scholarly journals Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing Solanum commersonii

Life ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 37
Author(s):  
Clizia Villano ◽  
Vincenzo D’Amelia ◽  
Salvatore Esposito ◽  
Maria Grazia Adelfi ◽  
Felice Contaldi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Segmental Duplications ◽  
Solanum Commersonii ◽  
Abiotic Stressors ◽  
Genome Wide ◽  
Specific Manner ◽  
Plant Families ◽  
Coa Reductase ◽  
Specific Pathway ◽  
Family Investigation

Steroidal glycoalkaloids (SGAs) are a class of nitrogen-containing glycosides occurring in several plant families and biosynthesized through a specific pathway. HMG-CoA reductase is the first enzyme of this pathway, and its transcription can be regulated by biotic and abiotic stressors and even in a tissue-specific manner. This study aimed to characterize the HMG genes family in a tuber-bearing potato species, Solanum commersonii, using transcriptional and functional approaches. Our results provided evidence that four ScHMGs with different tissue-specificities represent the HMG gene family in S. commersonii and that they originated from ScHMG1 through segmental duplications. Phylogenetic analysis suggests that ScHMG1 is the direct ortholog of AtHMG1, which is associated with SGAs accumulation in plants. Its overexpression in S. commersonii revealed that this gene plays a key role in the accumulation of glycoalkaloids regulating the production of dehydrocommersonine.

scholarly journals Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Vinicius Godoy Cerezer ◽  
Silvia Yumi Bando ◽  
Jacyr Pasternak ◽  
Marcia Regina Franzolin ◽  
Carlos Alberto Moreira-Filho
Keyword(s):  
Phylogenetic Analysis ◽  
Multidrug Resistance ◽  
Phylogenetic Profile ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Environmental Distribution ◽  
Pathogenic Potential ◽  
Clinical Strains ◽  
Specific Fragment ◽  
Clonal Variability

Stenotrophomonasssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species,S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates ofStenotrophomonasspp. and, environmental and clinical strains ofS. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process ofStenotrophomonasto different habitats. Two clinical isolates subgroups ofS. maltophiliasharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partialppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection withS. maltophiliawas nosocomial or community-acquired.

scholarly journals Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle

2014 ◽  
Vol 89 (2) ◽  
pp. 1036-1042 ◽  
Author(s):  
Emily A. Collin ◽  
Zizhang Sheng ◽  
Yuekun Lang ◽  
Wenjun Ma ◽  
Ben M. Hause ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Respiratory Disease ◽  
New Genus ◽  
Cross Reactivity ◽  
Surface Glycoprotein ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Antigenic Analysis ◽  
Pathogenic Potential

ABSTRACTViruses with approximately 50% homology to human influenza C virus (ICV) have recently been isolated from swine and cattle. The overall low homology to ICV, lack of antibody cross-reactivity to ICV in hemagglutination inhibition (HI) and agar gel immunodiffusion assays, and inability to productively reassort with ICV led to the proposal that these viruses represented a new genus of influenza virus, influenzavirus D (IDV). To further our understanding of the epidemiology of IDV, real-time reverse transcription-PCR was performed on a set of 208 samples from bovines with respiratory disease. Ten samples (4.8%) were positive and six viruses were successfully isolatedin vitro. Phylogenetic analysis of full-genome sequences of these six new viruses and four previously reported viruses revealed two distinct cocirculating lineages represented by D/swine/Oklahoma/1334/2011 (D/OK) and D/bovine/Oklahoma/660/2013 (D/660), which frequently reassorted with one another. Antigenic analysis using the HI assay and lineage-representative D/OK and D/660 antiserum found up to an approximate 10-fold loss in cross-reactivity against heterologous clade antiserum. One isolate, D/bovine/Texas/3-13/2011 (D/3-13), clustered with the D/660 lineage, but also had high HI titers to heterologous (D/OK) clade antiserum. Molecular modeling of the hemagglutinin esterase fusion protein of D/3-13 identified a mutation at position 212 as a possible antigenic determinant responsible for the discrepant HI results. These results suggest that IDV is common in bovines with respiratory disease and that at least two genetic and antigenically distinct clades cocirculate.IMPORTANCEA novel bovine influenza virus was recently identified. Detailed genetic and antigenic studies led to the proposal that this virus represents a new genus of influenza, influenzavirus D (IDV). Here, we show that IDV is common in clinical samples of bovine respiratory disease complex (BRDC), with a prevalence similar to that of other established BRDC etiological agents. These results are in good agreement with the near-ubiquitous seroprevalence of IDV previously found. Phylogenetic analysis of complete genome sequences found evidence for two distinct cocirculating lineages of IDV which freely reassort. Significant antigenic differences, which generally agreed with the surface glycoprotein hemagglutinin esterase phylogeny, were observed between the two lineages. Based on these results, and on the ability of IDV to infect and transmit in multiple mammalian species, additional studies to determine the pathogenic potential of IDV are warranted.

Gene loss in plants: Evidence from genome-wide phylogenetic analysis of thiamine pyrophosphate-dependent enzymes

2014 ◽  
Vol 53 (3) ◽  
pp. 221-227
Author(s):  
Xin-Min Tian ◽  
Peng Wang ◽  
Wen-Bin Hu ◽  
Da-Hai Gao ◽  
Qiong Li
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Thiamine Pyrophosphate ◽  
Genome Wide

scholarly journals Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum)

PLoS ONE ◽  
2020 ◽  
Vol 15 (7) ◽  
pp. e0236454 ◽  
Author(s):  
Essa Ali ◽  
Mohammad Ammar Raza ◽  
Ming Cai ◽  
Nazim Hussain ◽  
Ahmad Naeem Shahzad ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Linum Usitatissimum ◽  
Transcription Activator ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
Genome Wide Survey
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