genome evolution shweta menghani

7/27/2019 Genome Evolution Shweta Menghani

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GENOME EVOLUTIO

PRESENT

SHWETA MEN

A7110

M.Tech BIOTECHN

RD SE



“Genomes are more than instruction books for building and maintaining an oralso record the history of life.”



MUTATION AND RECOMBINATION provide the genome with the means to ev

• 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 t!ene loss %deletion)

*uestion +,here do genes "ome rom-

AIM: Understanding of mutation and recombination with comp

between the genomes of different organisms.

Answer + rom other genes



PolyploidyAneuploidyGenome reorganizationChromosomal mutationsGene uplicationGene !earrangement

"ransposons#orizontal gene transferGene e$pression%oss of gene function

HANISMS O" GENOME EV



POLYPLOIDY Wh#$e Ge%#&e

D'($)c*+)#%

Whole genome duplication is the process by which an organism’s entire genetic information isonce or multiple times which is known as polyploidy. This may provide an evolutionary benefit

organism by supplying it with multiple copies of a gene thus creating a greater possibility of fu

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 animal

• uplication of segments of (A is one of the greatest

sources of no&el traits.

duplication loss

ANEUPLOIDY



Chimps have an additional chromosome compared to hubecause the genetic material on human chromosome 2 i

between chimpanzee 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

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'inene amilies

Gene Duplication

http://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A10108/








There are two wa0s in whi"h rearrangement o domain#en"oding gene segments "an result

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







Exonduplica

Exonshuffling

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 genesTP gene as it exists to



• "hese are short se)uences that can mo&e from chromosome to c

• "ransposable elements ha&e a number of effects on e&olution of

as a whole. "he most significant of these is the ability of transpo

initiate recombination e&ents that lead to genome rearrangemen

• If they are produced during (A replication+ they are called tra

• If they are produced by an !(A intermediary ,!(A becomes te

(A+ not sent to ribosomes- they are called retrotransposons.

TRANSPOSONShe M#)$e DNA #- '&()%



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 transfer34ori(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 leastdistinctive 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 un"tion

Ola"tor0 re"eptor %OR) genes+ ina"tivation 'est e/planation or our reduo 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 fami

on chromosome ##

Duplication of

ancestral gene%utation in

both copies

Transposition to

different chromosomes

Further duplications

and mutations

E

& o l u t i o n a r ! t i m e

ζ

ε γ

ψθζ ψ'ψ

# ' # Gγ γ ψ δ

A model or the evolution o the human α#glo'in and β#glo'in gene amilies rom a sing

gene.



omparing genomes !entire *+A se(uences" of different speci

provides a powerful new tool for exploring the evolutionary dive

among organisms.

Genome sequencing and data collection hasadvanced rapidly in the last 25 years

Comparative studies of genomes• !dvance our understanding of the evolutiona

history of life

• "elp e#plain how the evolution of developmleads to morphological diversity

(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 m

insertions and deletions !indels"

4ostly differences in gene expression



Comparing istantly !elated /pecie

• "ighly conserved genes have changed very little o

• $hese help clarify relationships among species thadiverged from each other long ago

• %acteria& archaea& and eu'aryotes diverged from eother between 2 and ( billion years ago

• "ighly conserved genes can be studied in one modorganism& and the results applied to other organism



C#&(*-)% C$#e$3 Re$*+e S(ec

Genetic differences between closely relatedspecies can be correlated with phenotypicdifferences.

)everal genes are evolving faster in humans thanchimpanzees

$hese include genes involved in defense againstmalaria and tuberculosis and in regulation of brain

size& and genes that code for transcription factors



C#&(*-)% Ge%#&e W)+h)% * S(e

• !s a species& humans have only been around about

years and have low within+species genetic variation• ,ariation within humans is due to single nucleotide

polymorphisms& inversions& deletions& and duplicati• -ost surprising is the large number of copy+number• $hese variations are useful for studying human evo

human health



E&olutionar! biolog! is the stud! of the origin and descent of species) as well

o&er time* +nformatics has assisted e&olutionar! biologists in se&eral ke! wa!

researchers to-

• Trace the e&olution of a large number of organisms b! measuring changes

rather than through ph!sical taxonom! or ph!siological obser&ations alone)• %ore recentl!) compare entire genomes) which permits the stud! of more

e&olutionar! e&ents) such as gene duplication) hori/ontal gene transfer ) and

of factors important in bacterial speciation

• 0uild complex computational models of populations to predict the outcomo&er time

• Track and share information on an increasingl! large number of species an• Future work endea&ours to reconstruct the now more complex tree of life*

(omputational e&olutionar! biolog!

$/) 0 !$!%!))



• 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 wit

dierent genomes.

• Genome2iew: is a stand#alone se&uen"e 'rowser spe"ii"all0 designed to visualmanipulate a multitude o genomi"s data intera"tivel0.

• UC/C Genome 0rowser + on#line genome 'rowser hosted '0 the Universit0 o

Cru( %UC>C). It is an intera"tive we'site oering a""ess to genome se&uen"e da

o verte'rate and inverte'rate spe"ies and ma1or model organisms$ integrated wit

"olle"tion o aligned annotations.

$/) 0 !$!%!))



e&elopment of mathematical models that simulate the birth an

genes based on obser&ed age distributions of duplicated genes+ cboth small1scale+ continuously occurring local duplication e&ent

duplication e&ents affecting the whole genome. Application of th

showed that much of the genetic material in e$tant plants+ i.e.+ a

has been created by ancient genome duplication e&ents. More im

seems that a ma6or fraction of those genes could ha&e been retabecause it was created in large1scale gene duplication e&ents. In

transcription factors+ signal transducers+ and de&elopmental ge

ha&e been retained subse)uent to large1scale gene duplication e

RECENT DEVELOPMEN

"h # G th % t 7 Milli 8



"he #uman Genome: the %ast 7 Million 8ears

?o how different are we from the chimpan&ees@

!s far as our genomes are concerned the answer is about 1.54& this being the e#nucleotide sequence dissimilarity between humans and chimpanzees. 6ithin the cdifference is less than 1.54& with many genes having identical sequences in the tweven in the noncoding regions the dissimilarity is rarely more than 34.

i ti i B 7 i



ariation in Bene 7xpression

9nferred by comparing genes in different species6hy a chimpanzee develops into a cimpanzee a

not a human :;<.=4 of genes are >the same?@A!)8)ame genes are e#pressed but• !t different times• Bor different lengths of time• 9n different tissues

• 9n different amounts• 9n different combinations

#ample-icroarrays were used that contained 1<&*** human genes A8! isolatedchimp and human brains )ame genes were transcribed in both %ut pattelevels of transcription varied widely



It is clear, that what makes us human is probably not the human genom

the way in which the genome functions.



THAN5 YOU

genome evolution shweta menghani

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