Comparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan

(1) Background: Bacillus anthracis is a spore-forming, Gram-positive bacterium causing anthrax, a zoonosis affecting mainly livestock. When occasionally infecting humans, B. anthracis provokes three different clinical forms: cutaneous, digestive and inhalational anthrax. More recently, an injectional anthrax form has been described in intravenous drug users. (2) Case presentation: We report here the clinical and microbiological features, as well as the strain phylogenetic analysis, of the only injectional anthrax case observed in France so far. A 27-year-old patient presented a massive dermohypodermatitis with an extensive edema of the right arm, and the development of drug-resistant shocks. After three weeks in an intensive care unit, the patient recovered, but the microbiological identification of B. anthracis was achieved after a long delay. (3) Conclusions: Anthrax diagnostic may be difficult clinically and microbiologically. The phylogenetic analysis of the Bacillus anthracis strain PF1 confirmed its relatedness to the injectional anthrax European outbreak group-II.

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Genetic Diversity and Zoonotic Potential of Blastocystis in Korean Water Deer, Hydropotes inermis argyropus

Pathogens ◽

10.3390/pathogens9110955 ◽

2020 ◽

Vol 9 (11) ◽

pp. 955

Author(s):

Kyoo-Tae Kim ◽

Gyeonguk Noh ◽

Haeseung Lee ◽

Seon-Hee Kim ◽

Hyesung Jeong ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

18S Rrna ◽

Intestinal Tract ◽

Protozoan Parasite ◽

Domestic Animals ◽

Nucleotide Sequencing ◽

Zoonotic Potential ◽

Infection Status ◽

Korean Water Deer

Blastocystis is a protozoan parasite commonly detected in the intestinal tract of humans and animals. It has been actively studied worldwide; however, information on Blastocystis is limited in Korea. Because there is an increasing concern about the contact between wildlife and domestic animals or humans, we assessed the infection status and zoonotic potential of Blastocystis in Korean water deer (KWD, Hydropotes inermis argyropus) using genotyping and phylogenetic analysis. A total of 125 fresh fecal samples were collected from KWD which were killed by vehicles on highways or roadsides in this study. Among the 125 samples, 51 (40.8%) were PCR positive. We performed nucleotide sequencing and phylogenetic analysis of 26 of the 51 PCR-positive samples. By analyzing Blastocystis 18S rRNA, two subtypes (ST4 and ST14) were identified in this study. Of the 26 samples analyzed, 25 were identified as ST14 and one as ST4. Infection of ST14 in humans has not been reported. Although only one ST4 sample was detected in this study, ST4 has zoonotic potential without showing ruminant specificity. Thus, continuous attention should be provided to the potential of transmission between wildlife and domestic animals and humans.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00027-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 5951-5958 ◽

Cited By ~ 29

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.

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Genotypic characterization and phylogenetic analysis of Cryptosporidium sp. from domestic animals in Brazil

Veterinary Parasitology ◽

10.1016/j.vetpar.2007.08.018 ◽

2007 ◽

Vol 150 (1-2) ◽

pp. 65-74 ◽

Cited By ~ 45

Author(s):

F. Huber ◽

S. da Silva ◽

T.C.B. Bomfim ◽

K.R.S. Teixeira ◽

A.R. Bello

Keyword(s):

Phylogenetic Analysis ◽

Domestic Animals ◽

Genotypic Characterization

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Detection and phylogenetic analysis of a novel tick-borne virus in Haemaphysalis longicornis ticks and sheep from Shandong, China

Virology Journal ◽

10.1186/s12985-021-01704-y ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Lijun Shao ◽

Ruiheng Chang ◽

Lin Liu ◽

Yongjin Wang ◽

Yun Gao ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary Relationship ◽

Domestic Animals ◽

Molecular Evidence ◽

Haemaphysalis Longicornis ◽

Serum Samples ◽

Pathogenic Potential ◽

Qrt Pcr ◽

Positive Rate ◽

Yantai City

AbstractDabieshan tick virus (DTV) was first identified in Haemaphysalis longicornis from Hubei Province, China in 2015. However, its pathogenic potential to animals and human remains to be further explored. In this study, a total of 170 engorged ticks and 22 sheep serum samples were collected from Taian and Yantai city, Shandong Province to investigate the presence of DTV. The results of qRT-PCR revealed the positive rate of 13.6% (3/22) in sheep serum and 8.2% (14/170) in attached ticks, respectively. Phylogenetic analysis demonstrated a close evolutionary relationship among those DTV isolates from animal and ticks, and DTV might be relatively conservative in evolution. These findings are the first to demonstrate molecular evidence of DTV in domestic animals. Nonetheless, whether or not causing disease in animals, DTV deserves further investigation.

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Phylogenetic analysis of TALE superclass homeobox genes in amphipod crustaceans

10.1101/2021.08.10.455793 ◽

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.

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

10.21203/rs.2.15778/v1 ◽

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

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Comparative Insilco physiochemical and phylogenetic analysis of Insulin like growth factor 1 receptor (IGF-1R) in domestic animals

Indian Journal of Animal Research ◽

10.18805/ijar.b-3614 ◽

2018 ◽

Author(s):

P R. Sahoo ◽

G. Sahoo ◽

P. C. Behera

Keyword(s):

Phylogenetic Analysis ◽

Growth Factor ◽

Evolutionary Genetics ◽

Domestic Animals ◽

Amino Acid Sequences ◽

Insulin Like Growth Factor ◽

Multiple Sequence ◽

Lung Cancers ◽

Physiochemical Parameters ◽

Time Of Divergence

Insulin like growth factor 1receptors (IGF-1R) are the proteins which are expressed on the cell surface of almost all tissues in human as well as domestic animals with major involvement in growth, cancer, aging, production and in early embryonic development. Due to above importance, this protein needs to be characterized both in physiochemical and phylogenetically for further exploration in livestock research. In this study, the IGF1R amino acid sequences of selected domestic animals are retrieved from UniProt database and various physiochemical parameters were compared through ProtParam insilco tool. The multiple sequence alignment (MSA) and phylogenetic analysis was performed through Clustal omega and Molecular evolutionary genetics analysis (MEGA) application platform respectively. It was found that this protein is an unstable, hydrophilic in all domestic animals with amino acids varied from 1307 to 1412 in number. The phylogenetic analysis showed that highest time of divergence occurs in killer whale and rabbit, but least time of divergence occurs between goat and bovine. So this study will provide a better platform for the development of suitable anticancer therapeutics in domestic animals in nearest future as IGF-1R is implicated in several cancers, including breast, prostate, and lung cancers.

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In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

Indian Journal of Animal Research ◽

10.18805/ijar.b-3712 ◽

2019 ◽

Author(s):

P.R. Sahoo ◽

S.R. Mishra ◽

S. Mohapatra ◽

Santoswini Sahu ◽

G. Sahoo ◽

...

Keyword(s):

Phylogenetic Analysis ◽

In Silico ◽

Tertiary Structure ◽

Alpha Helix ◽

Domestic Animals ◽

Random Coil ◽

Local Alignment ◽

Physiochemical Properties ◽

Gapdh Gene ◽

Time Of Divergence

This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

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