GENOME EVOLUTION

PRESENTED BY:
SHWETA MENGHANI
A7110712004
M.Tech BIOTECHNOLOGY
RD SEM! AIB
Genomes are more than instruction books for building and maintaining an organism; they
also record the history of life.
MUTATION AND RECOMBINATION provide the genome with the means to evolve.

Evolution o genome arrangement
!ene order "hanges# Inversions$ translo"ations
Evolution o genome "ontent
!ene gain %se&uen"e divergen"e$ dupli"ation$ re"om'ination$ hori(ontal transer)
!ene loss %deletion)
*uestion +,here do genes "ome rom-
AIM: Understanding of mutation and recombination with comparisons
between the genomes of different organisms.
Answer + .rom other genes

Polyploidy

Aneuploidy

Genome reorganization

Chromosomal mutations

Gene uplication

Gene !earrangement

"ransposons

#orizontal gene transfer

Gene e$pression

%oss of gene function

MECHANISMS O" GENOME EVOLUTION
POLYPLOIDY
Wh#$e Ge%#&e
D'($)c*+)#%
Whole genome duplication is the process by which an organisms entire genetic information is copied,
once or multiple times which is known as polyploidy. This may provide an evolutionary benefit to the
organism by supplying it with multiple copies of a gene thus creating a greater possibility of functional and
selectively favored genes.
An example of extreme genome duplication is represented by the
ommon ordgrass !Spartina anglica" which is a dodecaploid,
meaning that it contains #$ sets of chromosomes

uplication or loss of an indi&idual chromosome'

Plants are able to tolerate aneuploidy better than animals'

uplication of segments of (A is one of the greatest

sources of no&el traits.
duplication loss
ANEUPLOI
DY
Chmps have an addtona chromosome compared to human
because the genetc matera on human chromosome 2 s spt
between chmpanzee chromosomes 12 and 13.
Ge%#&e Re,
#-.*%)/*+)#%
The dupli"ation o e/isting genes is almost "ertainl0 the most important pro"ess or the generation o new genes during
genome evolution. There are several wa0s in whi"h it "ould o""ur+
Une&ual "rossing#over
Une&ual sister "hromatid e/"hange
Repli"ation slippage
.igure+ !ene dupli"ations during the evolution o the human glo'in
gene amilies
Gene Duplication
There are two wa0s in whi"h rearrangement o domain#en"oding gene segments "an result in novel protein
un"tions+
Domain dupli"ation o""urs when the gene
segment "oding or a stru"tural domain is
dupli"ated '0 une&ual "rossing#over or
repli"ation slippage.

Domain shuling o""urs when segments
"oding or stru"tural domains rom
"ompletel0 dierent genes are 1oined
together to orm a new "oding se&uen"e
that spe"iies a h0'rid or mosai" protein$
one that would have a novel "om'ination
o stru"tural eatures and might provide
the "ell with an entirel0 new 'io"hemi"al
un"tion.
!earrangement of e$isting genes
Exon
duplication
Exon
shuffling
Exon
shuffling
F EGF K K
K
F F F F
EGF EGF EGF EGF
Epidermal growth
factor gene with multiple
EGF exons
Fibronectin gene with multiple
finger exons
Plasminogen gene with a
kringle exon
Portions of ancestral genes TP gene as it exists toda!
"hese are short se)uences that can mo&e from chromosome to chromosome*
"ransposable elements ha&e a number of effects on e&olution of the genome
as a whole. "he most significant of these is the ability of transposons to
initiate recombination e&ents that lead to genome rearrangements.
If they are produced during (A replication+ they are called transposons.
If they are produced by an !(A intermediary ,!(A becomes template for
(A+ not sent to ribosomes- they are called retrotransposons.
TRANSPOSONS
The M#0)$e DNA #- 1'&()%. .e%e2
Movement o transposons rom one site to another "an
also have an impa"t on genome evolution. .or e/ample$
The ei"ien"0 with whi"h DNA#'inding proteins that
are atta"hed to upstream regulator0 se&uen"es "an
a"tivate trans"ription o a gene might 'e ae"ted i a
transposon moves into a new site immediatel0
upstream o the gene
Trans"ription o the gene might also 'e inluen"ed '0
the presen"e o promoters and2or enhan"ers within the
transposon$ so the gene 'e"omes su'1e"t to an entirel0
new regulator0 regime
%ori&ontal or 'ateral gene transfer
34ori(ontal gene transer is a highl0 signii"ant phenomenon and
amongst single#"elled organisms perhaps the dominant orm o geneti" transer5
omparisons of bacterial and archaeal genome
se(uences suggest that lateral gene transfer has been a
ma)or event in the evolution of prokaryotic genomes. The
genomes of most bacteria and archaea contain at least a
few hundred kb of *+A, representing tens of genes, that
appears to have been ac(uired from a second prokaryote.
There are several mechanisms by which genes can be
transferred between prokaryotes,
on)ugation,
Transformation,
Transduction
-n plants, new genes can be ac(uired by llopol!ploid!,
which results from interbreeding between two different
species and can result in a viable hybrid.
.sually, the two species that form the allopolyploid are
closely related and have many genes in common, but
each parent will possess a few novel genes or at least
distinctive alleles of shared genes.
/or example, the bread wheat, Triticum aestivum, is a
hexaploid that arose by allopolyploidi&ation.
Allopolyploidi&ation can therefore be looked upon as a
combination of genome duplication and interspecies gene
transfer.
%oss of gene function:
.ay for genomes to e&ol&e
!ene ina"tivation results in pseudogenes.
Pseudogenes: se&uen"es o DNA that are similar to un"tional genes 'ut do not
un"tion
Ola"tor0 re"eptor %OR) genes+ ina"tivation 'est e/planation or our redu"ed sense
o smell
678 o human OR genes are ina"tive pseudogenes
9:78 gorilla ; "himpan(ee OR genes un"tion
9<:8 New ,orld mon=e0 OR genes wor= well
ncestral globin gene
"Globin gene famil!
on chromosome #$
"Globin gene famil!
on chromosome ##
Duplication of
ancestral gene
%utation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
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A model or the evolution o the human #glo'in and #glo'in gene amilies rom a single an"estral glo'in
gene.
omparing genomes !entire *+A se(uences" of different species
provides a powerful new tool for exploring the evolutionary divergence
among organisms.
Genome sequencng and data coecton has
advanced rapdy n the ast 25 years
Comparatve studes of genomes:
Advance our understandng of the evoutonary
hstory of fe
Hep expan how the evouton of deveopment
eads to morphoogca dversty
(omparati&e genomics
0'ast shared common ancestor 123 45A
0$26 human genes no counterparts in Fugu (75% are shared!!!)
07xtensive genome rearrangements since mammal lineage and teleost fish diverged
0%uman genome 896 repetitive *+A but only :6 of Fugu se(uence repetitive
0*iverged about 92 45A !;differences are miniscule<="
0%uman has 133 million more nucleotides than the mouse
0$2,333 genes and they share 886
0>33 genes uni(ue to either organism !#6"

*iverged 1.# 45A
#.26 difference in the se(uence, due mostly to
insertions and deletions !indels"
4ostly differences in gene expression not genes
Comparing istantly !elated /pecies
Hghy conserved genes have changed very tte over tme
These hep carfy reatonshps among speces that
dverged from each other ong ago
Bactera, archaea, and eukaryotes dverged from each
other between 2 and 4 bon years ago
Hghy conserved genes can be studed n one mode
organsm, and the resuts apped to other organsms
C#&(*-)%. C$#2e$3 Re$*+e4 S(ec)e2
Genetc dfferences between cosey reated
speces can be correated wth phenotypc
dfferences.
Severa genes are evovng faster n humans than
chmpanzees
These ncude genes nvoved n defense aganst
maara and tubercuoss and n reguaton of bran
sze, and genes that code for transcrpton factors
C#&(*-)%. Ge%#&e2 W)+h)% * S(ec)e2
As a speces, humans have ony been around about 200,000
years and have ow wthn-speces genetc varaton
Varaton wthn humans s due to snge nuceotde
poymorphsms, nversons, deetons, and dupcatons
Most surprsng s the arge number of copy-number varants
These varatons are usefu for studyng human evouton and
human heath
E&olutionar! biolog! is the stud! of the origin and descent of species) as well as their change
o&er time* +nformatics has assisted e&olutionar! biologists in se&eral ke! wa!s, it has enabled
researchers to-
Trace the e&olution of a large number of organisms b! measuring changes in their D.)
rather than through ph!sical taxonom! or ph!siological obser&ations alone)
%ore recentl!) compare entire genomes) which permits the stud! of more complex
e&olutionar! e&ents) such as gene duplication) hori/ontal gene transfer) and the prediction
of factors important in bacterial speciation
0uild complex computational models of populations to predict the outcome of the s!stem
o&er time
Track and share information on an increasingl! large number of species and organisms
Future work endea&ours to reconstruct the now more complex tree of life*
(omputational e&olutionar! biolog!
0last+ Genome blast: >e&uen"e alignment tools
"reecon: ?h0logeneti" anal0sis Tools
i1A#o!e: a highl0 sensitive tool to dete"t degenerated homolog0 relations within and 'etween
dierent genomes.
Genome2iew: is a stand#alone se&uen"e 'rowser spe"ii"all0 designed to visuali(e and
manipulate a multitude o genomi"s data intera"tivel0.
UC/C Genome 0rowser + on#line genome 'rowser hosted '0 the Universit0 o Caliornia$ >anta
Cru( %UC>C). It is an intera"tive we'site oering a""ess to genome se&uen"e data rom a variet0
o verte'rate and inverte'rate spe"ies and ma1or model organisms$ integrated with a large
"olle"tion o aligned annotations.
TOOLS & DATABASES
e&elopment of mathematical models that simulate the birth and death of
genes based on obser&ed age distributions of duplicated genes+ considering
both small1scale+ continuously occurring local duplication e&ents+ as well as
duplication e&ents affecting the whole genome. Application of this model
showed that much of the genetic material in e$tant plants+ i.e.+ about 345+
has been created by ancient genome duplication e&ents. More importantly+ it
seems that a ma6or fraction of those genes could ha&e been retained only
because it was created in large1scale gene duplication e&ents. In particular
transcription factors+ signal transducers+ and de&elopmental genes seem to
ha&e been retained subse)uent to large1scale gene duplication e&ents.
RECENT DEVELOPMENT
"he #uman Genome: the %ast 7 Million 8ears
?o how different are we from the chimpan&ees@
As far as our genomes are concerned the answer s about 1.5%, ths beng the extent of the
nuceotde sequence dssmarty between humans and chmpanzees. Wthn the codngDNAthe
dfference s ess than 1.5%, wth many genes havng dentca sequences n the two genomes, but
even n the noncodng regons the dssmarty s rarey more than 3%.
Aariation in Bene 7xpression
Inferred by comparng genes n dfferent speces
Why a chmpanzee deveops nto a cmpanzee and
not a human (98.7% of genes are "the same")
REASON:
Same genes are expressed but
At dfferent tmes
For dfferent engths of tme
In dfferent tssues
In dfferent amounts
In dfferent combnatons
Exampe:
Mcroarrays were used that contaned 18,000 human genes RNA soated from
chmp and human brans Same genes were transcrbed n both But patterns and
eves of transcrpton vared wdey
Itisclear,thatwhatmakesushumanisprobablynotthehumangenomeitself,but
thewayinwhichthegenomefunctions.
THAN5 YOU