Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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Isolation of DNA topoisomerase II gene from Pleurotus ostreatus and its application in phylogenetic analysis

Journal of Applied Microbiology ◽

10.1111/j.1365-2672.2007.03446.x ◽

2007 ◽

Vol 103 (5) ◽

pp. 2026-2032 ◽

Cited By ~ 2

Author(s):

C.X. Li ◽

J.X. Zhang ◽

C.Y. Huang ◽

Q. Chen ◽

H.X. Wang

Keyword(s):

Phylogenetic Analysis ◽

Pleurotus Ostreatus ◽

Topoisomerase Ii ◽

Dna Topoisomerase Ii ◽

Dna Topoisomerase

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The TOP2 gene of Trypanosoma brucei: a single-copy gene that shares extensive homology with other TOP2 genes encoding eukaryotic DNA topoisomerase II

Molecular and Biochemical Parasitology ◽

10.1016/0166-6851(90)90214-7 ◽

1990 ◽

Vol 38 (1) ◽

pp. 141-150 ◽

Cited By ~ 50

Author(s):

Phyllis R. Strauss ◽

James C. Wang

Keyword(s):

Trypanosoma Brucei ◽

Topoisomerase Ii ◽

Single Copy ◽

Single Copy Gene ◽

Dna Topoisomerase Ii ◽

Dna Topoisomerase ◽

Copy Gene ◽

Genes Encoding ◽

Eukaryotic Dna

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Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

PeerJ ◽

10.7717/peerj.10256 ◽

2020 ◽

Vol 8 ◽

pp. e10256

Author(s):

Lauren K. Hudson ◽

Lisha Constantine-Renna ◽

Linda Thomas ◽

Christina Moore ◽

Xiaorong Qian ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Population Structure ◽

Salmonella Enterica ◽

Genome Wide Association Study ◽

Phylogenetic Analyses ◽

Branch Length ◽

Human Infection ◽

Clinical Isolates ◽

Genes Encoding ◽

Allelic Differences

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

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Protein disulphide isomerase family in bread wheat (Triticum aestivum L.): genomic structure, synteny conservation and phylogenetic analysis

Plant Genetic Resources ◽

10.1017/s1479262111000232 ◽

2011 ◽

Vol 9 (2) ◽

pp. 342-346 ◽

Cited By ~ 1

Author(s):

E. d'Aloisio ◽

A. R. Paolacci ◽

A. P. Dhanapal ◽

O. A. Tanzarella ◽

E. Porceddu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Bread Wheat ◽

Plant Species ◽

Genomic Structure ◽

Triticum Aestivum L ◽

Protein Disulphide Isomerase ◽

Homoeologous Genes ◽

Genes Encoding ◽

High Level

Eight genes encoding protein disulphide isomerase (PDI)-like proteins in bread wheat were cloned and characterized and their genomic structure was compared with that of homoeologous genes isolated from other plant species. Fourteen wheat cDNA sequences of PDI-like genes were amplified and cloned; eight of them were relative to distinct PDI-like genes, whereas six corresponded to homoeologous sequences. Also, the genomic sequences of the eight non-homoeologous genes were amplified and cloned. Phylogenetic analysis, which included eight genes encoding PDI-like proteins and the gene encoding the typical PDI, assigned at least one of them to each of the eight major clades identified in the phylogenetic tree of the PDI gene family of plants. The close chromosome synteny between wheat and rice was confirmed by the location of the homoeologous genes of the PDI family in syntenic regions of the two species. Within the same phylogenetic group, a high level of conservation, in terms of sequence homology, genomic structure and domain organization, was detected between wheat and the other plant species. The high level of conservation of sequence and genomic organization within the PDI gene family, even between distant plant species, might be ascribed to the key metabolic roles of their protein products.

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Evidence for the Heterolobosea from Phylogenetic Analysis of Genes Encoding Glyceraldehyde-3-Phosphate Dehydrogenase

Journal of Eukaryotic Microbiology ◽

10.1111/j.1550-7408.1996.tb04507.x ◽

1996 ◽

Vol 43 (6) ◽

pp. 475-485 ◽

Cited By ~ 35

Author(s):

ANDREW J. ROGER ◽

MICHAEL W. SMITH ◽

RUSSELL F. DOOLITTLE ◽

W. FORD DOOLITTLE

Keyword(s):

Phylogenetic Analysis ◽

Genes Encoding

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Phylogenetic positions of several amitochondriate protozoa——Evidence from phylogenetic analysis of DNA topoisomerase II

Science in China Series C Life Sciences ◽

10.1360/04yc0111 ◽

2005 ◽

Vol 48 (6) ◽

pp. 565 ◽

Cited By ~ 3

Author(s):

De HE

Keyword(s):

Phylogenetic Analysis ◽

Topoisomerase Ii ◽

Dna Topoisomerase Ii ◽

Dna Topoisomerase

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Rotavirus G9P[4], G9P[6] and G1P[6] strains isolated from children with acute gastroenteritis in Pune, western India, 2013–2015: evidence for recombination in genes encoding VP3, VP4 and NSP1

Journal of General Virology ◽

10.1099/jgv.0.001323 ◽

2019 ◽

Vol 100 (12) ◽

pp. 1605-1630

Author(s):

Vaishali S. Tatte ◽

Deepthy Maran ◽

Atul M. Walimbe ◽

Varanasi Gopalkrishna

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Information ◽

Genetic Material ◽

Western India ◽

Full Genome ◽

Limited Data ◽

Structural Genes ◽

Genes Encoding ◽

Excellent Tool

Species A rotaviruses (RVAs) are genetically diverse pathogens. These are the most evolutionarily adaptable organisms, with a multitude of mechanisms for evolutionary change. To date, full-genome classification has been proved to be an excellent tool for studying the evolution of unusual rotavirus strains. As limited data are available from Pune (Maharashtra), western India, the current study was undertaken with the aim of understanding the genetic diversity in three (G1P[6], G9P[4] and G9P[4]) unusual RVA strains circulating in Pune, India during 2013–2015. Full-genome analysis of these strains classified them as G1-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, G9-P[4]-I2-R2-C2-[M1-M2_R]-[A1-A2_R]-N2-T2-E6-H2 and G9-[P4-P6_R]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequencing and phylogenetic analysis of the structural and non-structural genes of these unusual RVA strains showed nucleotide/amino acid identities of 82.3–98.5 %/77.3–99.8 % and 86.6–97.6 %/89.6–97.8 % between the strains of the study. Evidence of recombination events was found within the genes encoding VP3, VP4 and NSP1, which showed a combination of genetic information for genogroup 1 [M1/P[6]/A1] and genogroup 2 [M2/P[4]/A2] strains. This study will facilitate future investigations into the molecular pathogenesis of such RVAs as the exchange of whole or partial genetic material between rotaviruses through recombination contributes directly to their diversification, adaptation and evolution.

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