scholarly journals Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

2012 ◽  
Vol 8 ◽  
pp. EBO.S10048 ◽  
Author(s):  
Payal Singh ◽  
Supratim Sengupta
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Purine Riboswitch

scholarly journals Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories ofqnrBand Genetic Platforms within Particular Citrobacter Species

2015 ◽  
Vol 59 (10) ◽  
pp. 5951-5958 ◽  
Author(s):  
Teresa G. Ribeiro ◽  
Ângela Novais ◽  
Raquel Branquinho ◽  
Elisabete Machado ◽  
Luísa Peixe
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Pulsed Field Gel Electrophoresis ◽  
Divergent Evolution ◽  
High Identity ◽  
Content Type ◽  
Clonal Relatedness ◽  
Intergenic Regions ◽  
Genetic Sequences ◽  
Comparative Genomics Analysis

ABSTRACTTo gain insights into the diversification trajectories ofqnrBgenes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose,Citrobactersp. isolates (n= 21) and genome or plasmid sequences (n= 56) available in public databases harboring complete or truncatedqnrBgenes were analyzed.Citrobacterspecies identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location ofqnrBgenes, and the genetic surroundings ofqnrBgenes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification ofCitrobacterisolates was achieved usingleuSandrecNgene sequences, and isolates characterized in this study were diverse and harbored chromosomalqnrBgenes. Phylogenetic analysis of all knownqnrBgenes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprisingpspFandsapAand varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of theseqnrBclusters, and the reliable identification of allCitrobacterisolates revealed that each platform evolved in different recognizable (Citrobacter freundii,C. braakii,C. werkmanii, andC. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome ofCitrobacterspp. and in different plasmids ofEnterobacteriaceae. Our data corroborateCitrobacteras the origin ofqnrBand further suggest divergent evolution of closely relatedqnrBgenes/platforms in particularCitrobacterspp., which were delineated using particular genotypic markers.

scholarly journals Phylogenetic analysis of TALE superclass homeobox genes in amphipod crustaceans

2021 ◽  
Author(s):  
Wai Hoong Chang ◽  
Alvina G Lai
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Comparative Genomics ◽  
Homeobox Genes ◽  
Crustacean Species ◽  
Animal Development ◽  
Amphipod Crustacean

TALE class genes are a group of developmentally conserved transcription factors found in animals. Here, we describe the identification and phylogenetic analysis of TALE class genes in amphipod crustaceans. We identified 241 putative TALE class genes from 56 amphipod crustacean species. Phylogenetic analysis of the genes revealed six subclasses. We provide a list of FASTA sequences of the genes identified. Results from this work may inform future evolutionary and comparative genomics studies on animal development.

scholarly journals Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

2019 ◽  
Author(s):  
Meng Chen ◽  
Chun-Yang Xu ◽  
Xu Wang ◽  
Chong-Yang Ren ◽  
Jiao Ding ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Environmental Changes ◽  
Guanosine Monophosphate ◽  
Cyanobacterial Blooms ◽  
Medium Size ◽  
Pan Genome ◽  
Diguanylate Cyclases ◽  
Comparative Genomics Analysis

Abstract Background: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. Results: General characterization along with a pan-genome analysis showed that M. aeruginosa have a medium size genome (4.99 Mb in average), a conserved core genome, and an expansive pan-genome. Phylogenetic analysis showed good overall congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and pan-genome matrix. Furthermore, phylogenetic analysis revealed no correlation between geographic distribution and phylogenetic relationships of the M. aeruginosa strains isolated from different regions. Moreover, proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. It was revealed that the numbers of genes that encode diguanylate cyclases, phosphodiesterases, and hybrid proteins with GGDEF-EAL domains in M. aeruginosa might result from environment-specific adaptation. Bioinformatics and structure analysis of c-di-GMP signal-related GGDEF, EAL and GGDEF-EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. Conclusions: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidate the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism. Keywords: Microcystis aeruginosa, Comparative genomics, c-di-GMP, Phylogenetic analysis, GGDEF, EAL, PilZ

scholarly journals Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

2020 ◽  
Author(s):  
Meng Chen ◽  
Chun-Yang Xu ◽  
Xu Wang ◽  
Chong-Yang Ren ◽  
Jiao Ding ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Second Messengers ◽  
Guanosine Monophosphate ◽  
Cyanobacterial Blooms ◽  
Pan Genome ◽  
Comparative Genomics Analysis

Abstract Background: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. Results: Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.99 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good overall congruence between the three types of phylogenetic trees based on 31 highly conserved protein-coding genes, sensor domain-coding genes, and pan-genome matrix. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. Conclusions: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism. Keywords: Microcystis aeruginosa, Comparative genomics, c-di-GMP, Phylogenetic analysis, GGDEF, EAL, HD-GYP, PilZ

scholarly journals Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O. I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Gene Family ◽  
Perennial Ryegrass ◽  
Plant Architecture ◽  
Foxtail Millet ◽  
Grass Species ◽  
Plant Type ◽  
Bac Clone

Perennial ryegrass is an important pasture grass in temperate regions. As a forage biomass-generating species, plant architecture-related characters provide key objectives for breeding improvement. In silico comparative genomics analysis predicted colocation between a previously identified QTL for plant type (erect versus prostrate growth) and the ortholocus of the rice OsABCG5 gene (LpABCG5), as well as related QTLs in other Poaceae species. Sequencing of an LpABCG5-containing BAC clone identified presence of a paralogue (LpABCG6) in the vicinity of the LpABCG5 locus, in addition to three other gene-like sequences. Comparative genomics involving five other 5 grass species (rice, Brachypodium, sorghum, maize, and foxtail millet) revealed conserved microsynteny in the ABCG5 ortholocus-flanking region. Gene expression profiling and phylogenetic analysis suggested that the two paralogues are functionally distinct. Fourteen additional ABCG5 gene family members, which may interact with the LpABCG5 gene, were identified through sequencing of transcriptomes from perennial ryegrass leaf, anther, and pistils. A larger-scale phylogenetic analysis of the ABCG gene family suggested conservation between major branches of the Poaceae family. This study identified the LpABCG5 gene as a candidate for the plant type determinant, suggesting that manipulation of gene expression may provide valuable phenotypes for perennial ryegrass breeding.

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