scholarly journals In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Genes ◽  
2018 ◽  
Vol 9 (6) ◽  
pp. 284 ◽  
Author(s):  
Gökhan Karakülah ◽  
Athanasia Pavlopoulou
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
In Silico

Phylogenetic Analysis of Mos1-Like Transposable Elements in the Drosophilidae

1999 ◽  
Vol 49 (6) ◽  
pp. 760-768 ◽  
Author(s):  
Frédéric Brunet ◽  
Fabienne Godin ◽  
Claude Bazin ◽  
Pierre Capy
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements

scholarly journals In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Eva Bauwens ◽  
Myrthe Joosten ◽  
Joemar Taganna ◽  
Mirko Rossi ◽  
Ayla Debraekeleer ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
In Silico

scholarly journals Truncated Non-Nuclear Transposable Elements in Grapevine: A Mini Review

2019 ◽  
Vol 50 (4) ◽  
pp. 219-227
Author(s):  
A.V. Milovanov ◽  
J. Tello ◽  
U.C.M. Anhalt ◽  
A. Forneck
Keyword(s):  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Transposable Elements ◽  
Vitis Vinifera ◽  
In Silico ◽  
Gene Evolution ◽  
High Rate ◽  
Miniature Inverted Transposable Elements ◽  
High Level ◽  
Inner Region

Abstract In this mini-review we present insight to the non-nuclear transposable elements and in silico analysis of miniature inverted transposable elements (MITEs) in the grapevine mitochondrial genome. Here we report the identification of 17 truncated sequences in grapevine (Vitis vinifera L.) mitochondrial genome which expectedly belongs to the four ancient transposon families (hAT, Tc1Mariner, Mutator and PIF/Harbinger). Some sequences with a high rate of homology in chloroplast and nuclear genomes were also identified. Thus, it suggests the intercellular gene transfer between these three organelles. These partial sequences showed a high level of similitude with full MITE sequences, and they were found in their inner region, supporting their MITE origin. Further analysis revealed these sequences in other life kingdoms (including eubacteria and archaea), which indicates their ancient origin. Further research showed that 13 out of the 17 sequences are conserved domains of the genes where they are located, suggesting their contribution to gene evolution. Therefore, we suppose that more studies of nature, origin and functional meaning of these sequences and their fusion with genes are necessary. In the light of our observations it will be useful for further studies of V. vinifera genome organizing and systematics, as well as for other species.

scholarly journals Characterization and Genomic Analysis of ValSw3-3, a New Siphoviridae Bacteriophage Infecting Vibrio alginolyticus

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Ling Chen ◽  
Quan Liu ◽  
Jiqiang Fan ◽  
Tingwei Yan ◽  
Haoran Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Bacterial Infections ◽  
Phage Therapy ◽  
Gc Content ◽  
Vibrio Alginolyticus ◽  
Lytic Bacteriophage ◽  
Sequence Alignments ◽  
Content Type ◽  
Link Type

ABSTRACT A novel lytic bacteriophage, ValSw3-3, which efficiently infects pathogenic strains of Vibrio alginolyticus, was isolated from sewage water and characterized by microbiological and in silico genomic analyses. Transmission electron microscopy indicated that ValSw3-3 has the morphology of siphoviruses. This phage can infect four species in the Vibrio genus and has a latent period of 15 min and a burst size of 95 ± 2 PFU/infected bacterium. Genome sequencing results show that ValSw3-3 has a 39,846-bp double-stranded DNA genome with a GC content of 43.1%. The similarity between the genome sequences of ValSw3-3 and those of other phages recorded in the GenBank database was below 50% (42%), suggesting that ValSw3-3 significantly differs from previously reported phages at the DNA level. Multiple genome comparisons and phylogenetic analysis based on the major capsid protein revealed that phage ValSw3-3 is grouped in a clade with five other phages, including Listonella phage phiHSIC (GenBank accession no. NC_006953.1), Vibrio phage P23 (MK097141.1), Vibrio phage pYD8-B (NC_021561.1), Vibrio phage 2E1 (KX507045.1), and Vibrio phage 12G5 (HQ632860.1), and is distinct from all known genera within the Siphoviridae family that have been ratified by the International Committee on Taxonomy of Viruses (ICTV). An in silico proteomic comparison of diverse phages from the Siphoviridae family supported this clustering result and suggested that ValSw3-3, phiHSIC, P23, pYD8-B, 2E1, and 12G5 should be classified as a novel genus cluster of Siphoviridae. A subsequent analysis of core genes also revealed the common genes shared within this new cluster. Overall, these results provide a characterization of Vibrio phage ValSw3-3 and support our proposal of a new viral genus within the family Siphoviridae. IMPORTANCE Phage therapy has been considered a potential alternative to antibiotic therapy in treating bacterial infections. For controlling the vibriosis-causing pathogen Vibrio alginolyticus, well-documented phage candidates are still lacking. Here, we characterize a novel lytic Vibrio phage, ValSw3-3, based on its morphology, host range and infectivity, growth characteristics, stability under various conditions, and genomic features. Our results show that ValSw3-3 could be a potent candidate for phage therapy to treat V. alginolyticus infections due to its stronger infectivity and better pH and thermal stability than those of previously reported Vibrio phages. Moreover, genome sequence alignments, phylogenetic analysis, in silico proteomic comparison, and core gene analysis all support that this novel phage, ValSw3-3, and five unclassified phages form a clade distant from those of other known genera ratified by the ICTV. Thus, we propose a new viral genus within the Siphoviridae family to accommodate this clade, with ValSw3-3 as a representative member.

scholarly journals Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Carolina Chiellini ◽  
Renato Iannelli ◽  
Franco Verni ◽  
Giulio Petroni
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Biology ◽  
16S Rrna ◽  
Bacterial Communities ◽  
In Silico ◽  
Pollution Levels ◽  
High Pollution ◽  
Seabed Sediments ◽  
Bacterial Groups ◽  
Different Levels

Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries andin silicodigestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled within silicodigestion of the obtained sequences evidenced the dominance ofProteobacteriaand the high percentage ofBacteroidetesin all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.

scholarly journals Identification in silico and expression analysis of a β-1-4-endoglucanase and β-galactosidase genes related to ripening in guava fruit

2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Mario A. Mejía-Mendoza ◽  
Cristina Garcidueñas-Piña ◽  
José S. Padilla-Ramírez ◽  
Ruth E. Soria-Guerra ◽  
José Francisco Morales-Domínguez
Keyword(s):  
Phylogenetic Analysis ◽  
Cell Wall ◽  
Expression Analysis ◽  
In Silico ◽  
The Other ◽  
Homologous Sequence ◽  
Plant Tissues ◽  
Fruit Softening ◽  
Guava Fruit ◽  
Putative Protein

Abstract Background Guava fruit softening is a crucial process during ripening and this process involves a number of enzymes that modifies the cell wall. Two of the enzymes that regulate this process are (a) the β-1, 4-endoglucanase 17 (BEG) which hydrolyze β-1, 4 bonds from cellulose and hemicellulose, and (b) β-galactosidase (BGA) that hydrolyzes pectin chains. Bioinformatics and expression analysis information on these genes is limited in guava fruit. Results A fragment of a β-1, 4-endoglucanase 17 (PgE17), and another of a β-galactosidase (PgGa1) were identified. These sequences have a similarity of more than 85% with those reported in the NCBI database. In the guava genome, one homologous sequence was found for PgE17 in Chr 4 and two homologous to PgGa1: one in Chr 3 and the other one in Chr 6. Putative protein PgE17 contains part of the glyco_hydro_9 domain. Putative protein PgGa1 has a part of the glyco_hydro_35 domain. Phylogenetic analysis of PgE17 and PgGa1 revealed that both are highly conserved inside the Myrtaceae family. In silico expression analysis showed that both PgE17 and PgGa1 work in a coordinated way with other cell wall modifier enzymes. Expression of these genes was found in all the guava samples analyzed. However, the highest expression was found in the fruit in the breaking and ripe states. Conclusions A β-1, 4-endoglucanase 17, and β-galactosidase 1 sequences were identified. PgE17 and PgGa1 are expressed in all the plant tissues, and fruit ripening states. Although, the highest expression was on breaker and ripe states.

Sign in / Sign up

Export Citation Format

Share Document