Faculty Opinions recommendation of Phylogenetic analysis based on genome-scale metabolic pathway reaction content.

Anthropogenic activities have increased the amount of urban wastewater discharged into natural aquatic reservoirs containing a high amount of nutrients such as phosphorus (Pi and PO 4 − 3 ), nitrogen (NH 3 and NO 3 − ) and organic contaminants. Most of the urban wastewater in Mexico do not receive any treatment to remove nutrients. Several studies have reported that an alternative to reduce those contaminants is using consortiums of microalgae and endogenous bacteria. In this research, a genome-scale biochemical reaction network is reconstructed for the co-culture between the microalga Chlorella vulgaris and the bacterium Pseudomonas aeruginosa. Metabolic Pathway Analysis (MPA), is applied to understand the metabolic capabilities of the co-culture and to elucidate the best conditions in removing nutrients. Theoretical yields for phosphorus removal under photoheterotrophic conditions are calculated, determining their values as 0.042 mmol of PO 4 − 3 per g DW of C. vulgaris, 19.43 mmol of phosphorus (Pi) per g DW of C. vulgaris and 4.90 mmol of phosphorus (Pi) per g DW of P. aeruginosa. Similarly, according to the genome-scale biochemical reaction network the theoretical yields for nitrogen removal are 10.3 mmol of NH 3 per g DW of P. aeruginosa and 7.19 mmol of NO 3 − per g DW of C. vulgaris. Thus, this research proves the metabolic capacity of these microorganisms in removing nutrients and their theoretical yields are calculated.

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Metabolic Pathway Analysis for Nutrient Removal of the Consortium between C. vulgaris and P. aeruginosa

10.20944/preprints201903.0002.v1 ◽

2019 ◽

Author(s):

A. Suggey Guerra-Rentería ◽

Mario García-Ramírez ◽

César Gómez-Hermosillo ◽

Abril Goméz-Guzmán ◽

Yolanda González-García ◽

...

Keyword(s):

Pathway Analysis ◽

Metabolic Pathway ◽

Anthropogenic Activities ◽

Reaction Network ◽

Inorganic Phosphorus ◽

Biochemical Reaction ◽

Metabolic Pathway Analysis ◽

Biochemical Reaction Network ◽

A Genome ◽

Genome Scale

Anthropogenic activities have increased the amount of urban wastewater discharged into natural aquatic reservoirs confining in them a high amount of nutrients and organics contaminants. Several studies have reported that an alternative to reduce those contaminants is using consortiums of microalgae and endogenous bacteria. In this research, a genome-scale biochemical reaction network is reconstructed for the co-culture between the microalga Chlorella vulgaris and the bacterium Pesudomonas aeruginosa. Metabolic Pathway Analysis (MPA), is applied to understand the metabolic capabilities of the co-culture and to elucidate the best conditions in removing nutrients such as Phosphorus (inorganic phosphorous and phosphate) and Nitrogen (nitrates and ammonia). Theoretical yields for Phosphorus removal under photoheterotrophic conditions are calculated, determining their values as 0.042 mmol of PO4/ g DW of C. vulgaris, 19.53 mmol of inorganic Phosphorus /g DW of C. vulgaris and 4.90 mmol of inorganic Phosphorus/ g DW of P. aeruginosa. Similarly, according to the genome-scale biochemical reaction network the theoretical yields for Nitrogen removal are 10.3 mmol of NH3/g DW of P. aeruginosa and 7.19 mmol of NO3 /g DW of C. vulgaris. Thus, this research proves the metabolic capacity of these microorganisms in removing nutrients and their theoretical yields are calculated.

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Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda

10.22541/au.163272382.29563626/v1 ◽

2021 ◽

Author(s):

Qing Zuo ◽

Zhisheng Zhang ◽

Yanjun Shen

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Divergence Time ◽

Gene Arrangement ◽

Phylogenetic Study ◽

Relationship Of ◽

Genome Scale ◽

The Relationship

The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda and Pauropoda), but very little work has been done to explore their phylogenetic relationships. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within Myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

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Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Archaea ◽

10.1155/2017/9763848 ◽

2017 ◽

Vol 2017 ◽

pp. 1-18 ◽

Cited By ~ 14

Author(s):

ShengShee Thor ◽

Joseph R. Peterson ◽

Zaida Luthey-Schulten

Keyword(s):

Metabolic Pathway ◽

Metabolic Modeling ◽

Knowledge Bases ◽

Sequencing Data ◽

Growth Requirements ◽

Archaeal Species ◽

Evolution Of Metabolism ◽

Engineering Modeling ◽

Genome Scale ◽

Insight Into

Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism’s biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.

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Reconstruction of genome-scale metabolic pathway in Aspergillus terreus NIH2624

2011 3rd International Conference on Electronics Computer Technology ◽

10.1109/icectech.2011.5942064 ◽

2011 ◽

Author(s):

Thankaswamy Kosalai Subazini ◽

Gopal Ramesh Kumar

Keyword(s):

Metabolic Pathway ◽

Aspergillus Terreus ◽

Genome Scale

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ECO-MP: E coli-Metabolic Pathway-development of Genome-scale Metabolic Pathway Database for Escherichia coli

Trends in Bioinformatics ◽

10.3923/tb.2014.7.12 ◽

2014 ◽

Vol 7 (1) ◽

pp. 7-12

Author(s):

Gopal Ramesh Kum ◽

Thankaswamy Kosalai Su ◽

Ashok Selvaraj

Keyword(s):

Escherichia Coli ◽

Metabolic Pathway ◽

Pathway Database ◽

E Coli ◽

Genome Scale

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Whole-genome-based phylogeny of African swine fever virus

Veterinary World ◽

10.14202/vetworld.2020.2118-2125 ◽

2020 ◽

Vol 13 (10) ◽

pp. 2118-2125

Author(s):

Levon Aslanyan ◽

Hranush Avagyan ◽

Zaven Karalyan

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Phylogenetic Trees ◽

Evolutionary Dynamics ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Fever Virus ◽

A Genome ◽

Genotype 2 ◽

Genome Scale

Aim: A genome-scale phylogenetic analysis was used to infer the evolutionary dynamics of Asfarviridae – African swine fever virus (ASFV) – and better define its genetic diversity. Materials and Methods: All complete ASFV genomes from NCBI's resource as of March 2020 were used. The phylogenetic analysis used maximum likelihood and neighbor-joining methods. The evolutionary models detection was done with the help of the package of programs MEGA-X. Algorithms were used to build phylogenetic trees for type B DNA polymerases of ASFV (n=34) and HcDNAV (n=2), as an external group. Results: An expedient categorization of the Asfarviridae family uses five clades. Genotype 1 (except for LIV 5/40 virus isolate) as well genotype 7 are assigned to the alpha clade; genotype 2 to the beta clade; genotypes 8, 9, and 10 to the gamma clade; genotype 5 to the delta clade; and genotypes 3, 4, and 20, as well as genotype 22 and the LIV 5/40 isolate to the epsilon clade. Branch lengths on the phylogenetic tree are proportional to genetic distance along the branch. Branches at the phylogenetic tree of Asfarviridae are much shorter than branches for Baculoviridae. Shorter branches in ASFVs population suggest that Asfarviridae evolved relatively recently and remain more closely related. Conclusion: We suggest applying more robust standards using whole genomes to ensure the correct classification of ASFV and maintain phylogeny as a useful tool.

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