This document contains questions submitted by a student for their PhD dissertation discussion. It includes questions about evolution, genome evolution, gene migration, DNA mutation, intron evolution, genome size variation, gene duplication, and references related to these topics. Experimental evidence is discussed for endosymbiotic theory, chloroplast and mitochondria DNA originating from bacteria, and gene migration between organelle and nuclear genomes.

1. Submitted to:-
Dr. Puspendra Kumar
Associate Professor
Dept. of Agril. Biotechnology
Submitted by:-
Abhishek singh
Ph.D. Agril. Biotechnology
ID 4243
II semester

2. Discussion questions
1. What is Evolution ?
2. Impotent theory and experiment related to evolution.
3. What is Genome evolution ?
4. What is gene migration and its experimental evidence
5. DNA Sequences evolve by mutation?
6. How did Interrupted genes Evolve ?
7. Why are some genome so large and smaller ?
8. Gene Duplication contributes to genome evolution.
9. Genome duplication has played a role in plant evolution.

3. What is Evolution ?
• Evolution is the change in the characteristics of a species over several generation.

4. Impotent Era of evolution
• The earth formed 4.6 billion year ago from the solar nebula.
• By the end of the hadean Era, 3.8 billion year ago the
atmosphere was rich in carbon dioxide and water vapor but
had no oxygen gas and no protective ozone layer.
• Over next 2 billion year the evolution of oxygenic
photosynthetic and gradual oxidation of the oceans
resultation of oxygen in the atmosphere.
• Photosynthetic bacterial cells had probably evolved by 3.8 to
3.5 billion year ago and oxygen producing photosynthesis was
wide spared by 2.2 billion year ago.
• Eukaryotic organism had evolved by 2.7 billion year ago.

6. Impotent theory and experiment related to evolution of
photosynthetic Eukaryotic organism .
Symbiogenesis, or endosymbiotic theory, is an evolutionary theory of the origin of
Eukaryotic cells from Prokaryotic organisms, Given by Lynn Margulis in 1967.She
was an American evolutionary theorist and biologist. The Endosymbiotic theory
divided into two events:
A.First endosymbiotic event: engulfment of a bacterium (the alfa- proteobacterium)by
another prokaryotic host cell. The resulting proto-eukaryotic cell underwent
transfer of gene from the genome of the engulfed cell to the host-cell genome and
conversion of the engulfed cell to a specialized subcellular compartment
(organelle)-the mitochondria. The host-cell genome become enclosed in
membrane, giving rise to rise nucleus.
B. The second endosymbiotic event : a eukaryotic cell engulfed cell a prokaryotic ,
photosynthetic cyanobacterium. Transfer of genes from the engulfed cell to the
host nucleus then took place, together with conversion of engulfed cell to a
specialized organelle.
c. The original photosynthetic eukaryotic organism gave rise to three clades of
organisms present today : Glaucophytes , Red alage , Green alage

7. Source : Biochemistry and molecular biology of plant Buchanan.

8. video link : https://youtu.be/L_QYz6-mz4w
Source: McGraw-Hill Animations Published on Jun 6, 2017

9. •With the use of antibiotic prove that Mitochondria genome and Chloroplast genome
evolved from bacteria. Here we use chloramphenicol to inhibited protein synthesis in
Chloroplast and Mitochondria as they inhibited into bacteria.
Source : Lumen microbiology

10. What is Genome evolution ?
1. Genome evolution is the process by which a genome change
in structure(sequence) or size over time.
2. The growing number of complete genome seq has provided
valuable opportunities to study genome structure and
organization.
3. Genome sequencing provided opportunities to information-
• Gene distribution.
• The proportions of nonrepetitive and repetitive DNA and
there function potentials.
• Number of copies of repetitive seq.

11. Predicted function of Arabidopsis: (A) Proportion of gene in different functional categories.
(B) Proportion of gene in various organism that have strong similarity to Arabidopsis in each
functional category.

12. What is gene migration and its experimental evidence
1. The evolutionary history of Plant cell involves at least two
independent endosymbiotic events.
2. Over evolutionary time, most of its gene (Chloroplast and
Mitrochondrion) transferred to the genome of the host
cell,which became enclosed in a memebrane to form the
nucleus of the cell.
3. Plant Nuclear genome has characteristics that indicate a
joint archeal and bacterial heritage.
4. Plant Nuclear genome of plastide also know as Chimeric
Genome because it containing both the elements of the
proto-eukaryotic genome and elements derived from the
cyanobacterial genome.

13. • There is some question arise related to Plant Genome
evolution
1. Photosystem Two have two componet core complex and
Antenna complex, core complex have membrane protein
D1 it attached with pigment PQ-B and coded by Psb-a
gene which regulated by chloroplast genome?
2. core complex have another membrane protein D2 it
attached with pigment PQ-A and coded by Psb-b gene
which regulated by Nuclear genome genome why?
3. Rubisco is Holoenzyme or conjugated enzyme which have
two subunit Larger subunit(rbc-L) encoded by Chloroplast
genome and smaller subunit (rbc-S)encoded by nuclear
genome why?
4. For Expression of Rubisco required Light why?
5. Chloroplast protein encoded by Nuclear gene ?

15. ATP
Synthesis

17. •In addition to the nucleus, chloroplasts and mitochondria also have a genome.
Genes can migrate from these organelles into the nucleus. Ralph Bock from the
Max Planck Institute for Molecular Plant Physiology in Potsdam, Germany,
investigates the mechanisms of this migration by simulating evolution in the lab.
•Video: https://youtu.be/bGdbYIa95KQ?list=LL5yclIdu_AxDvVYq9k7s2gA
Source : Max plant institute of molecular plant physiology.

18. DNA Sequences evolve by mutation
• Mutation is change in Nucleotide seq of DNA . Mutation occurs when DNA
is altered by replication error or chemical change to nucleotide , or when
electromagnetic break or form chemical bonds and the damage remains
unrepaired at the time of next DNA replication event
• Spontaneous mutations often occur which can cause various changes in
the genome. Mutations can either change the identity of one or more
nucleotides, or result in the addition or deletion of one or more
nucleotide bases. Such changes can lead to a Frameshift mutation ,
causing the entire code to be read in a different order from the original,
often resulting in a protein becoming non-functional.
• A mutation in a promoter region, enhancer region or transcription
factor binding region can also result in either a loss of function, or an up or
downregulation in the transcription of the gene targeted by these
regulatory elements.
• Mutations are constantly occurring in an organism's genome and can
cause either a negative effect, positive effect or neutral effect

19. • If a mutation occurs in the coding region of a
protein- coding gene, it can be characterized by
its effect on the polypeptide product of the
gene. This mutation are divided into two types:
1. Synonymous mutation- Mutation that does not
change the amino acid sequence of the
polypeptide product. It is specific type of silent
mutation.
2. Nonsynonymous mutation- This type of
mutation coding region does not alter the amino
acid seq of the polypeptide product , creating
either a missense codon or a
nonsense(Termination) codon.

20. How did Interrupted genes Evolve ?
• A major evolutionary question is whether gene originated is whether gene originated with introns or whether
they were originally uninterrupted.
• Interrupted gene that correspond either to protein or to independently funcationing non- protein-encoding RNAs
probably originated in an interrupted form(The “introns early hypothesis”)
• The interruption allowed base order to better satisfy the potential for stem-loop extrusion from duplex DNA .
• The structure of many eukaryotic gene suggests a concept of the eukaryotic genome as a sea of mostly unique
DNA seq in which exon “island” separated by intron “shallows”are strung out in individual gene “archipelagoes”
What was the original form of gene ?
1. Introns eraly model – This model proposal that introns have always been an integral part of the gene. Gene
originated as interrupted structure and those now without intron have lost them in course of evolution.
2. Intron late model- This model suggested that the ancestral proteon coding seq were uninterrupted and that
intron were subsequently inserted into them.
Intron play important role in interrupted gene evolve lossing and gain of intron introduced new characters into
organism this lossing and gaining of intron due to selection pressures.Example of this is:
1. Bird tend to have shorter introns than mammals which has led to controversial hypothesis that there has
selection pressure for compaction of the genome because of the metabolic demand of flight.
2. Many microorganism (such Yeast and Bacteria) evolutionary success can be equated with ability to rapidly
replicate DNA.Smaller genome can be more rapidly replicated than larger so it may be the pressure for
compaction of genome that led uniinterupted genes in most microorganism
3. Vertebrate mitochondial genome are very small and extremely compact wheres yeast mitocondrial genome are
larger and have some complex interrupted genes .

21. Exon shuffling
• Exon shuffling is a theory, introduced by Walter Gilbert in 1977
• Exon shuffling is a mechanism by which new genes are created. This can
occur when two or more exons from different genes are combined together
or when exons are duplicated. Exon shuffling results in new genes by altering
the current intron-exon structure.
• This can occur by any of the following processes:
1. transposon mediated shuffling.
2. sexual recombination or non-homologous recombination (also called
illegitimate recombination).
• Exon shuffling may introduce new genes into the genome that can be either
selected against and deleted or selectively favored and conserved Example
The process of blood coagulation and fibrinolysis invovled a complex
cascade of enzymatic reaction in which inactive zymogens belong are
converted into active enzyme, And Mosaic protein or chimeric protein is
created when an exon from one gene is integrated into another gene’s
intron.

22. Why are some genome so large and smaller ?
• The genomes of most eukaryotes are larger and more complex than those
of prokaryotes
• discovery that the genomes of most eukaryotic cells contain not only
functional genes but also large amounts of DNA sequences that do not
code for proteins.The difference in the sizes of the salamander and human
genomes thus reflects larger amounts of non-coding DNA, rather than more
genes, in the genome of the salamander. The presence of large amounts of
noncoding sequences is a general property of the genomes of complex
eukaryotes. Thus, the thousandfold greater size of the human genome
compared to that of E. colis not due solely to a larger number of human
genes. The human genome is thought to contain approximately 100,000
genes—only about 25 times more than E. coli has. Much of the complexity
of eukaryotic genomes thus results from the abundance of several different
types of noncoding sequences, which constitute most of the DNA of higher
eukaryotic cells.
• In Alternative splicing also a key factor for reduced the complexity in
different organism.

23. Gene Duplication contributes to genome evolution.
• Gene duplication is the process by which a region of DNA coding for a gene is
duplicated. This can occur as the result of an error, in recombination or through
a retrotransposition event. Duplicate genes are often immune to the selective
pressure under which genes normally exist. As a result, a large number of
mutations may accumulate in the duplicate gene code. This may render the gene
non-functional or in some cases confer some benefit to the organism.
• The cause of gene duplication one of the gene copies may be inactivated by an
epigenetic mechanism or by mutation. However when both copies remain active
they fulfill the function of a single gene in ancestral plant. consequently if one of
gene is lost by mutation the other member of pair can compensate for its
absence and no phenotype change occur .If both gene are lost by muation then
compensation protein is available and a mutant phenotype is observed .
• When the function of two or more gene overlaps in this way the gene are said to
be “Functionally redundant” eg SHP-1 and SHP-2 gene these gene control
formation of elongated fruit in Arabidopsis. The loss of one of these gene by
mutation does not result in formation of defective fruit –one gene can
compensate for absense of another. It is only when both gene are mutated that
abnormal fruit development development occur.

24. Source : Smith.M Alison (2015) Plant Biology. Garland science Tatlor & Francis,2.

25. REFERENCES
• Smith.M Alison (2015) Plant Biology. Garland science Tatlor & Francis,2.
• Singh B. D. (2012). Biotechnology Expanding horizons. Kalyani publishers, 4.
• Buchanan.Bob B (2007) Biochemistry and Moelcular biology of pant.I.K.International,2.
• Krebes.Jocelyn E (2011) Lewin’s Gene. Jonand and Bartlett Publishers,10.
• Primrose.S.B and Twyman.R.M(2014). Principle of gene manipulation and genomics. Wiley
blackwell,7.
• Vijay Dalal, Shlomi Dagan, Gilgi Friedlander, Elinor Aviv, Ralph Bock, Dana Charuvi, Ziv Reich2 &
Zach Adam(2018) Transcriptome analysis highlights nuclear control of chloroplast development in
the shoot apex.Science reporter
• Wesite: Max plant institute of molecular plant physiology.
• Wikipedia