Bacterial Genomes and Pan Genomes

This article discusses the concept of bacterial genomes and pan genomes, their variations in gene content, and their implications in bacterial evolution and adaptation. It explores the use of gene sequencing and metagenomics in studying the pan-genome. The article also highlights the differences in genome size and gene content among bacterial species and the relationship between genome size and the number of genes. It concludes with a discussion on genetic nomenclature and the use of identifiers for genes and proteins. Find study material, solved assignments, and essays on bacterial genomes and pan genomes at Desklib.

BACTERIAL GENOMES AND PAN GENOMES 1
Bacterial Genomes and Pan Genomes
Student’s Name
Institution Affiliate
Date

BACTERIAL GENOMES AND PAN GENOMES 2
Introduction
A complete set of genes in an organism is called a genome. A bacterial genome is thus
generally composed of single and circular chromosomes. Bacterial strains belonging to the same
species vary considerably in gene content. The pan-genome is much larger than the gene content
of individual strains. The variation in DNA materials in addition to other differences in genomic
structure and nucleotide polymorphism among strains confer upon prokaryotic species a
phenomenal adaptability. Since the method of gene sequencing, multiple strains from a single
species is the primary and easiest way to study the pan-genome, feasible alternatives include
those related to DNA hybridization. Also, the use of metagenomics sequences is also applicable
by data mining from the growing metagenomics database. The pan-genome concept has
significant consequences for the way of understanding bacterial evolution, adaptation, and
population structure as well as more applied issues such as vaccine design or the identification of
virulence genes.
The sizes of the bacterial genomes are variant and mostly they are smaller species than
the animal and unit cell eukaryotes when compared. Its size ranges from about 130 millimeters,
and its size expands at a relatively slower rate in eukaryotes than prokaryotes. The number of
DNA that are non-coding increases with size of the genome more rapid in non-bacteria than in
bacteria (Roach et al., 2015). This agrees with the concept that several eukaryote DNA does not
code, on the other hand, some eukaryotic, organelles and viral genes code. There exist almost
over fifty phyla of bacteria different from each other eleven of which are phyla of archaeal. The
immediate generation from the first produced draft genomes nearly ninety percent of genomes n
GenBank are by now incomplete.

BACTERIAL GENOMES AND PAN GENOMES 3
The sequencing of the third generation produced complete genome in a few hours. Much
diversity in the structure has been revealed by genome sequencing. Over 2000 analysis of
Escherichia Coli genome generates an E. Coli core genome of about 3100 gene families and a
maximally 89000 several other families of genes (Rouli et al., 2015). Genome sequencing shows
that parasitic bacteria have 1500-2700 genes decompose especially when leprosy bacillus is
compared to ancestral bacteria. Researches have proved that most bacteria have smaller genomes
compare to their ancestors. In the past, studies have explained the general trend of bacterial
genome decomposition and the small sizes of the bacterial genomes. Laboratory report shows
that the parent breakdown of bacterial genome is due to deletion of bias.
Over thirty thousand sequenced bacterial genomes are available publicly and thousands
of metagenomes projects were availed since 2014. The comparison of single gene is now being
replaced by more less specific methods which have led to a novel perspective on relationships of
genes that were earlier estimated (Roach et al., 2015). The production of the metagenomics data
has been the significant achievement of the bacterial genome sequencing of the DNA present in
the sample in the second decade. Bacteria possess genome that is compact distinct from
eukaryotes in two different ways: bacteria are strongly correlation in the size and number of
genes that are functional in the genome as the genes are built in operons. The main purpose for
comparing the respective density of bacterial genome to genomes of eukaryotes for the
multicellular eukaryotes in the form of antigenic regions in the presence of noncoding DNA and
introns.
Observable expectations include pathogenic bacteria that were recently formed. This was
elaborated in a study by Cole et al. where the Mycobacterium leprae was discovered to have a
notable higher count of pseudogenes to functional genes at a proximately 40% than its free-living

BACTERIAL GENOMES AND PAN GENOMES 4
ancestors. Moreover, there is comparatively little difference in genome size when estimated with
the genome sizes of significant groups of life in species if bacteria. When considering the
quantity of genes present in eukaryotic species and genome size is little relevant. However, the
strong relationship between the size of the genome and the number of genes make the size of the
bacteria genome an exciting topic of discussion and research. The overall trend of bacteria
development indicates that bacteria began as a free living organism.
Some paths of evolution have resulted in certain bacteria becoming pathogens and
symbionts. In inclusion of a data that is functional on protein database, the transmission of a
historical data containing a protein that is functional into a list of annotation that is challenging
and lubricious particularly during the characterization of biochemical that has been reported with
non-reference of a sequence of a genome as was indicated in the previous years of study of DNA
(Salipante et al., 2015). Therefore, researchers should be granted an opportunity to put much
more entry of data and reference that are both functional. This can result in a variety of
designations of gene especially of that of identical and homologous genes indifferent database
and publications of a variety of strains of species that are similar when the enzymes that have
been coded and also possess an identity sequence of approximately 90 percent. The architecture
module that is identical are considered comparable to biochemical characteristics hence function.
The lifestyle of a bacteria plays a significant duty in their corresponding genome sizes
where the free living bacteria have largest genomes out of the three types of bacteria,
nevertheless, they have lesser pseudogenes than the bacteria that have recently acquired
pathogenicity. Facultative and recently evolved pathogenic bacteria have a smaller genome size
than free-living bacteria, yet they contain more pseudogenes than any other kind of bacteria. Of

BACTERIAL GENOMES AND PAN GENOMES 5
the three groups, pathogens have fewer genomes and fewest pseudogenes. In a comparison of a
single gene, a phylogeny of bacteria genome has improved in accuracy.
The average method of identifying nucleotides measures the genetic distance between all
genomes by taking advantage of regions of about 10000 boiling points algorithms are performed
to classify species. This has been performed for Pseudomonas avallanae species. A large amount
of information is lost during the transition of bacteria from free living parasitic life cycle to
lifelong host dependent life. Phylogenic studies have elaborated that mycoplasmas presented an
evolutionary derived state contrary to earlier hypothesis (Andreani, Hesse, & Vos, 2017). It is
clear that mycoplasmas are just one example of many of genome shrinkage in obligatory host-
association.
Primarily, a cell is a fundamental unit of life. The operating system of the cell genome sequence
was a long time ago considered to be a tedious task. It has been under study to come up with
code systems that could help interpret the genes for both eukaryotes and prokaryotes to give the
genetic functions. The inventory of genetic software of bacteria cell by the elimination of inating
genes that are not very much very necessary for cell growth and evolution.
Each genome facilitates the structural functions that are comparable for both molecular
and biological function of every genome to all forms of life. In strategy for whole gene synthesis,
overlapping oligonucleotides were designed, chemically synthesized and assembled in red
fragments (Salipante et al., 2015). After error correction and amplification, five fragments were
assembled blue cassettes which were verified and then assembled in yeast to generate one-eighth
green molecule. The eight molecules were amplified and then assembled in yeas to generate the
complete genome which is orange in color. Genes with insertion included genes that were

BACTERIAL GENOMES AND PAN GENOMES 6
subsequently characterized a quasi-essential I-genes, and some deletion of gene sections were
nonviable.
Retained quasi-essential genes yielded viable fragments with no viable complete genome
which necessitated the improvement of the software. In a few cases, then-genes were retained
chemically since their biological functions appeared essential. The upstream as well as the
downstream expressions of genes were preserved from the deletion region (Roach et al., 2015).
Since the key products of genes are typically functional units that are centrally placed living
organisms and very essential for a growing science field and biochemical applications, for
comprehension purposes, every gene required to be given a particular identity for its special
recognition for easy referencing worldwide (Rouli et al., 2015).
In the past the identification of genes was done through a resultant phenotype as well via
mutation, thus each was given a name containing a gene. However recently, the identification is
done on the basis of a sequences conducted through reading of the frames openly. The
expression of each genes is scrutinized using molecular techniques which include, deleting
mDNA in transcriptomics or protains in proteomics (Loman & Pallen, 2015). A bioinformatical
similarity method with an existing sequence identified in other living things deduces the putative
function of the protein. Every particular gene together with the molecular as well as its
organismic origin is identified by a high-quality identifier and should be consistent all the time in
all database. On addition of new data, an identifier should be updated, and it should as well
incorporate new data (Page et al., 2015).
In the same way, a gene can be defined by an identifier associated with groups that are
functional and readily reveal an idea on the biological role that is unequivocal and recognizable .
It should link scientists and researchers worldwide for consensus purposes

BACTERIAL GENOMES AND PAN GENOMES 7
Genetic nomenclature guides for microorganism groups have been established and
granted an opportunity worldwide by the society of biological science. The rules used to name
various genes of bacteria vary from those of genes of eukaryotic bacteria thus offering a
particular level of certainty of adaptation to a variety of needs (Ding, Baumdicker & Neher,
2017). It is to define the genes containing bacteria with those of the italised letters of the three
lower case that invokes an acronym the pathway or the mechanism that is biological to allow the
involvement of a gene. An upper-case latter then follows the three letters for
the particular gene in the route of the allele. An example is, celA for the first gene
identified in the degradation of cellulose.
In gene encoded protein situations, the gene name is used for the proteins that have been
encoded. The general steps on how to access the PGA web are summarized as follows: firstly,
select the module for the pan-genomic analysis according to data type and research objectives.
Secondly, input data for pan-Genome should be selected and uploaded. In this stage, the module
requires nucleotide annotations and protein sequence files for each strain. Finally, is the output
description which contains five parts: orthologous clustering, pan-genome profile, evolutionary
analysis, sequence variation analysis, and functional classification. These descriptions are given
to develop usability of the machine to create a friendly and easy to operate gadget that helps to
analyze the pan-genome accurately. This was a fast and freely available online server, in
incorporating the integration of previously published software such as PGAP, PanGP, and
PGAP-X. Briefly,PGA web is a user-friendly web interface, one-click input data submission and
for smooth and
efficient data analysis.

BACTERIAL GENOMES AND PAN GENOMES 8
The key variance relating to notation arguable is that the protein containing bacteria with
the three letters are not written in italics. However, there is only the capitalization of the first
letter. For science group that works together with the genes of eukaryotic including those of
different proteins identification conversions have been suggested. It is acceptable to apply the
genes that are identical as well as the identifiers of proteins to identify identical functions in
different strains (Ding, Baumdicker & Neher, 2017). Such as, lac is cross the boundaries of
genes are used in the designation of a lactose bacteria containing a gene for the route of
utilization or bgl for a β-glucosidase gene. The identification of glycosyl hydrolases also has
previously been customized in database as well as the publications to use the policies to curb the
problems associated with the few number of the three letters that are meaningful combinations
for numerous orthologous gene recognized in a variety of a thousands of genomes that are new
and sequenced (Land et al., 2015).
According to Chen & Shapiro (2015), to the protein, the species designator is combined
together with a Bg1A CLOTH for β-glucosidase where Bg1A is from Clostridium thermocellum
during the comparison of genes with those functions that are comparable existing among a
variety of species, and there is the use of a prefix. Adding a prefix to a gene name that defines a
family of gene has been developed for the study society. Enzymatic mechanism and certain
protein folding of the specific family which the amino acid sequence defines (Cury et al., 2016).
Some genes with comparable functions have multiple designations. There should be a
compatibility of the method of design with the traditional ones and should have particular task.
Clearly stated justifications and open discussion should be permitted for wide acceptance in the
international conferences.

BACTERIAL GENOMES AND PAN GENOMES 9
In the latter case, there arose some unique problems with the proteins of the multi-
modular. During the creation of designation of a new gene from a sequence, the genes containing
the same pose of proteins have similar difficulties that is a result of availability of enzyme
modules that could happen in the diverse functions of other genes. The same problem is also
seen in bacteria with extracellular and in pathway proteins of biosynthetic (Bazinet, 2017). The
proteins can be stable in globular parts and can refold autonomously to carry out specific
functions as opposed to enzyme amino acid stretching in the folding unit of a polypeptide and
contain particular functions they are typically eliminated from the other using linkers to allow the
stretching of the amino acids. Underlying codon usage principles was also tested using the
mycoids genome which has extremely high adenine and thymine content, M. mycoids uses codon
for the amino acid tryptophan, instead of a stop codon and occasionally uses nonstandard start
codons. In addition, the codon usage is highly biased towards high AT content. We can modify
this uncommon codon usage in regions of the three essential genes and to determine their roles.
Non-catalytic modules can also result in substrate binding. Bacteria also can secrete
enzymes which contain one or more catalytic modules of the non-analytic modules, and they
contain two independently active catalytic modules that supplement each other's activity such as
β-1,4-endoxylanase (Chaudhari, Gupta & Dutta, 2016). A gene or protein can theoretically be
named after the function of any other module. Among other rules and guidelines for naming
genomes which after research and proper normalization, are recorded in the software upon which
reference can be done and further modifications can be made should need be. Genomics is
slowly moving from a descriptive phase in which genomes are sequenced and analyzed to a
synthetic phase where whole genomes and proved nonviable even though one segment is
functional when tested in the context of the other seven segments. There lacked sufficient

BACTERIAL GENOMES AND PAN GENOMES 10
knowledge of designing a minimal functional genome from the first principles. Thus to come up
with better information concerning gene essentiality, the significant improvement was in the
mutagenesis method. To produce a genome containing all the essential and quasi-essential genes,
there was developed a DBT cycle for bacterial genomes. Any design is viable or not, can be built
in yeast and tested to determine whether it can function as a genome of a viable bacterium. The
aim is to obtain all the complete eight segments fully analyzed and the application of the whole
genome DBT cycle to a specific problem, the construction of a minimal cellular genome.
However, the approach applied can as well be used in the construction of a cell with any desired
properties.
The databases and sequences of the proteins are an inseparable mechanism for the
biologists. They should be made in such a way that information labeled is correct and accurate to
be relied on by the researchers. When the data sequence is manually curated, no particular
information has to be lost during the updates of the database and it should be transmitted to a
sequence of the strain of the minimum species available for a study (Andreani, Hesse, & Vos,
2017). Protein sequence database and a number of nucleotides are existing to help in the work of
microbiology that is molecular where an information concerning the structure of protein and the
genes are gathered, and the evidence obtained from an experiment for one characterization can
be located in crosslinks.
The compatibility of the web server is open to many platforms, including Firefox, Opera,
Internet Explorer, Chrome and Safari, using Bootstrap Framework as the front end program. It
adopted HTML5 and CCS3 protocol that applies D3.js and Escharts for result interaction. The
server back-end adopts an express framework for Node.js MongoDB which is used for storage-

BACTERIAL GENOMES AND PAN GENOMES 11
related information. A packaging code and software container is known as Docker is as well used
thus improving compatibility, portability, and safety. The website is free for all users and login is
not required for the PGA web.
Conclusion
From the discussion, bacteria genomes and pan genomes are a set of genes in an
organism. There are a number of differences existing between the two genomes. For example, a
bacterial genome is thus generally composed of single and circular chromosomes. Bacterial
strains belonging to the same species vary considerably in gene content. However, the pan-
genome is much larger than the gene content of single strains. The variation in DNA materials in
addition to other differences in genomic structure and nucleotide polymorphism among strains
confer upon prokaryotic species a phenomenal adaptability.
The other difference relies on the arrangement of the sequences of proteins in DNA. For
example, in the bacterial genome, the arrangement of the protein is such that the three letters are
not written in italics while there is the capitalization of the first letter. However, for pan-genome
that works together with the genes of eukaryotic bacteria as well as different naming of protein
conversions have been accepted to assist in the arrangement of the sequence of proteins in DNA.
The mentioned sequence of proteins in DNA is used as a tool by the biologists; thus they should
be labeled correctly and adequately to be used in the conduction of a variety of research.

BACTERIAL GENOMES AND PAN GENOMES 12
References
Andreani, N. A., Hesse, E., & Vos, M. (2017). Prokaryote genome fluidity is dependent on
effective population size. The ISME journal, 11(7), 1719.
Bazinet, A. L. (2017). Pan-genome and phylogeny of Bacillus cereus sensu lato. BMC
evolutionary biology, 17(1), 176.
Chaudhari, N. M., Gupta, V. K., & Dutta, C. (2016). BPGA-an ultra-fast pan-genome analysis
pipeline. Scientific reports, 6, 24373.
Chen, P. E., & Shapiro, B. J. (2015). The advent of genome-wide association studies for
bacteria. Current opinion in microbiology, 25, 17-24.
Cury, J., Jové, T., Touchon, M., Néron, B., & Rocha, E. P. (2016). Identification and analysis of
integrons and cassette arrays in bacterial genomes. Nucleic acids research, 44(10), 4539-
4550.
Ding, W., Baumdicker, F., & Neher, R. A. (2017). panX: pan-genome analysis and
exploration. Nucleic acids research, 46(1), e5-e5.
Fullmer, M. S., Soucy, S. M., & Gogarten, J. P. (2015). The pan-genome as a shared genomic
resource: mutual cheating, cooperation and the black queen hypothesis. Frontiers in
microbiology, 6, 728.
Land, M., Hauser, L., Jun, S. R., Nookaew, I., Leuze, M. R., Ahn, T. H., ... & Poudel, S. (2015).
Insights from 20 years of bacterial genome sequencing. Functional & integrative
genomics, 15(2), 141-161.
Loman, N. J., & Pallen, M. J. (2015). Twenty years of bacterial genome sequencing. Nature
Reviews Microbiology, 13(12), 787.

BACTERIAL GENOMES AND PAN GENOMES 13
Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T., ... & Parkhill, J.
(2015). Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31(22),
3691-3693.
Roach, D. J., Burton, J. N., Lee, C., Stackhouse, B., Butler-Wu, S. M., Cookson, B. T., ... &
Salipante, S. J. (2015). A year of infection in the intensive care unit: prospective whole
genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel
microbiota. PLoS genetics, 11(7), e1005413.
Rouli, L., Merhej, V., Fournier, P. E., & Raoult, D. (2015). The bacterial pangenome as a new
tool for analysing pathogenic bacteria. New microbes and new infections, 7, 72-85.
Salipante, S. J., Roach, D. J., Kitzman, J. O., Snyder, M. W., Stackhouse, B., Butler-Wu, S.
M., ... & Shendure, J. (2015). Large-scale genomic sequencing of extraintestinal
pathogenic Escherichia coli strains. Genome research, 25(1), 119-128.