5. Evolutionary genomics

2018 ◽  
pp. 59-87
Author(s):  
John Archibald
Keyword(s):  
Mitochondrial Dna ◽  
Amino Acid ◽  
Ancient Dna ◽  
Genomic Research ◽  
Evolutionary Genomics ◽  
Eukaryotic Cells ◽  
Comparative Genomic ◽  
Molecular Clocks ◽  
Genome Sequences ◽  
Protein Amino Acid

We are still learning how to make sense of what genome sequences have to tell us. ‘Evolutionary genomics’ first considers the ‘molecular clock’, a bedrock concept underlying modern comparative genomic research. Molecular clocks can be inferred using both protein (amino acid) and DNA (nucleotide) sequences. It then looks at our understanding of Y-chromosome and mitochondrial DNA evolution before discussing the difficulties of extracting ancient DNA from fossils. Among the most remarkable achievements of ancient DNA research has been the sequencing of nuclear genomes from Neanderthals and other now-extinct human relatives, aiding research into what makes us human. The question of how eukaryotic cells evolved from prokaryotes is also considered.

scholarly journals Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences

2020 ◽  
Author(s):  
Babatunde Olarenwaju Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Paul Akiniyi Akinduti ◽  
Babatunde Adebiyi Olusola ◽  
Olumide T Aerege ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Spike Protein ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Amino Acid ◽  
Protein Variant ◽  
Health Crisis ◽  
Most Recent Common Ancestor

ABSTRACTThe ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 × 10−4 high posterior density HPD (4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.

scholarly journals Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

2019 ◽  
Author(s):  
Ruimin Gao ◽  
Sohail Naushad ◽  
Sylvain Moineau ◽  
Lawrence Goodridge ◽  
Dele Ogunremi
Keyword(s):  
Amino Acid ◽  
Salmonella Enterica ◽  
Rational Design ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Practical Applications

Abstract Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages. Conclusions: Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.

scholarly journals Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

2020 ◽  
Author(s):  
Ruimin Gao ◽  
Sohail Naushad ◽  
Sylvain Moineau ◽  
Roger Levesque ◽  
Lawrence Goodridge ◽  
...  
Keyword(s):  
Amino Acid ◽  
Salmonella Enterica ◽  
Rational Design ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Practical Applications

Abstract Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages. Conclusions: Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.

scholarly journals Complete Genome Sequences of Two Escherichia Phages Isolated from Wastewater in Finland

2018 ◽  
Vol 6 (22) ◽  
Author(s):  
Saija Kiljunen ◽  
Anu Wicklund ◽  
Mikael Skurnik
Keyword(s):  
Amino Acid ◽  
Complete Genome ◽  
Amino Acid Sequences ◽  
Genome Sequences ◽  
Protein Amino Acid ◽  
Content Type ◽  
Tail Protein

ABSTRACT Escherichia phages vB_EcoM-fFiEco06 and vB_EcoM-fHoEco02 were found to have 167,076-bp and 167,064-bp genomes, respectively. They are members of genus T4virus, and they are 99.96% identical to each other. The host ranges of the phages are different, probably due to a few differences in their tail protein amino acid sequences.

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

scholarly journals Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Sara Jones ◽  
Raji Prasad ◽  
Anjana S. Nair ◽  
Sanjai Dharmaseelan ◽  
Remya Usha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Analysis ◽  
Influenza A ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
H1n1 Pandemic ◽  
Genome Sequences ◽  
Influenza A H1n1 ◽  
Virus Isolates ◽  
New Mutations

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

Isolation from atelia herbert-smithii pittier (sophoreae, leguminosae) and x-ray structure of cis-1-amino-3-hydroxymethyl-cyclobutane-1-carboxylic acid, an achiral non-protein amino acid

Tetrahedron ◽  
1987 ◽  
Vol 43 (8) ◽  
pp. 1857-1861 ◽  
Author(s):  
Geoffrey N. Austin ◽  
Peter D. Baird ◽  
Hak-Fun Chow ◽  
L.E. Fellows ◽  
G.W.J. Fleet ◽  
...  
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Protein Amino Acid ◽  
X Ray
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