Lecture 7: Genomes and their evolution

Question 1

Genome:

Answer 1

is the complete set of genes in an organism or the total genetic content in one set of chromosomes

Question 2

Genomics:

Answer 2

is the study of whole sets of genes and their interactions

Question 3

Comparative genomics:

Answer 3

is the analysis & comparison of genomes from different species

Question 4

Genome sequencing: most ambitious sequencing project to date:

Answer 4

the Human Genome Project which began in 1990 and was completed by 2003

Question 5

Genome sequencing:

Chimpanzee genome was completed by

Answer 5

2005 & today many more genomes have been completely sequences

Question 6

Human genome sequencing project originally took

Answer 6

13 years at a cost of $1 billion

Question 7

In 2008 Illumina sequencing of human genome costs

Answer 7

$350,000

Question 8

in 2014 Illumina annonced they could sequence human genome for

Answer 8

$1000

Question 9

It is now possible to generate hundreds of gigabases of data very quickly, however:

Answer 9

assembling genomes and annotated genomes still takes a long time.
- Computational and bioinformatic analyses lag behind our ability to generate data.

Question 10

How many genomes have been sequenced to date? By 2016..

Answer 10

the genomes of more than 14,000 different organisms had been sequenced and another many more are in the process of being sequenced.

Question 11

Many of the sequences genomes are

Answer 11

bacterial & archeal genomes. Approx 10& are eukaryotes, an include vertebrates, invertebrates, protists, fungi & plants

Question 12

Where are genomes sequenced?

Answer 12

• Genomes are sequenced by a variety of public and private organisations e.g.
  – National Human Genome Research Institute (NHGRI)
  – The Institute for Genomic Research (TIGR)
  – The Wellcome Trust Sanger Institute
  – JGI – DOE Joint Genome Institute
  – Private companies e.g. Syngenta/Monsanto
  – Research lab in Universities, Research Institute

Question 13

How is genome sequencing prioritised?

Answer 13

• The priority-setting process is based on the medical, agricultural and biological opportunities expected to be created by sequencing a given organism

Question 14

Genomes vary in:

Answer 14

SIZE

Question 15

genomes of most bacteria range from

Answer 15

1 to 6 million base pairs (Mb)

Question 16

Eukaryotic genomes are __ than bacteria

Answer 16

larger

Question 17

most multicellular animals & plants have genomes with at least

Answer 17

100 Mb

Question 18

fruit fly genome has how many base pairs?

Answer 18

165 Mb

Question 19

Human genome number of base pairs

Answer 19

3,000 Mb

Question 20

The genome of the single- celled yeast S. cerevisiae has about __ Mb

Answer 20

12 Mb

Question 21

Within each kingdom/domain there is __ systematic relationship between _____ & ____

Answer 21

no
genome size
phenotype

Question 22

Genomes vary in the number of

Answer 22

genes they contain

Question 23

Free-living bacteria and archaea have ___ genes

Answer 23

1,500 to 7,500

Question 24

The number of genes in eukaryotes ranges from

Answer 24

about 5000 (e.g. the unicellular yeast) to at least 40,000 genes in multicellular eukaryotes

Question 25

The number of genes is / is not correlated with genome size

Answer 25

IS NOT e. g. - the nematode worm C. elegans has 100 Mb genome and 20,000 genes - Drosophilahas165Mb genome and 13,700 genes

Question 26

Eukaryotic genomescna produce more than one polypeptide per

Answer 26

gene because of alternative splicing of RNA transcripts

Question 27

Gene diversity:

Answer 27

the number of genes presenting a given length of DNA

Question 28

In bacterial genomes most of the DNA consists of

Answer 28

genes coding for proteins, tRNA or rRNA

Question 29

Most eukaryotic DNA does

Answer 29

not code for protein and is not transcribed into functional RNA molecules.

Question 30

Humans have ___ times as much noncoding DNA as bacteria

Answer 30

10,000

Question 31

Multicellular eukaryotes have introns and a vast amount of

Answer 31

non-protein coding DNA between genes.

Question 32

"junk DNA" is thought to play important roles in the cell for example

Answer 32

* For example, the genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding regions. * The sesequences are more highly conserved than protein-coding genes in these species

Question 33

Only __ of the human genome codes for proteins or produces rRNAs and tRNAs

Answer 33

1.5%

Question 34

Gene-relatedregulatory sequences and introns account for, respectively __% and __% of the human genome.

Answer 34

5% | 20%

Question 35

Intergenic DNA is

Answer 35

Noncoding DNA found between genes - Pseudogenes - Repetitive DNA

Question 36

Pseudogenes are

Answer 36

former genes that have accumulated mutations and are nonfunctional

Question 37

Repetitive DNA is

Answer 37

is present in multiple copies in the genome

Question 38

About __% of repetitive DNA is made up of transposable elements

Answer 38

44%

Question 39

Comparative genomics

Answer 39

is the analysis and comparison of genomes from different species

Question 40

Comparative genomics allows us to

Answer 40

* Gain a better understanding of how species have evolved * Help explain how the evolution of development leads to morphological diversity * Determine the function of genes and non- coding regions of the genome

Question 41

Genome researchers look at many different features when comparing genomes:

Answer 41

– sequence similarity, – gene location, – the length and number of coding regions (exons) within genes, – the amount of noncoding DNA in each genome, – highly conserved regions maintained in organisms as simple as bacteria and as complex as humans.

Question 42

comparative genomics involves the use of

Answer 42

computer programs that can line up multiple genomes and look for regions of similarity among them. Some of these sequence-alignments tools are accessible to the public over the Internet.

Question 43

Comparative genomics can begin to address a range of questions e.g.

Answer 43

* Which sets of genes are common to many different organisms, or groups of organisms. * Which genes are unique?What do these genes do? * Which genes are necessary for multicellular life forms; which set of genes are only found in multicellular organisms but not in unicellular ones? * Where and how have new genes emerged in evolutionary history?

Question 44

Genome comparisons of distantly related species help us

Answer 44

understand ancient evolutionary events

Question 45

Genome comparisons of closely related species help us

Answer 45

understand recent evolutionary events

Question 46

Highly conserved genes that have changed very little over time help clarify relationships among species that

Answer 46

diverged from each other long ago.

Question 47

Archaea and bacteria diverged from each other between

Answer 47

2 & 4 billion years ago - know this form DNA sequencing

Question 48

Highly conserved genes can be studied in one model organism, and the results

Answer 48

applied to other organisms

Question 49

Orthologs are

Answer 49

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. • Normally, orthologs retain the same function in the course of evolution.

Question 50

60 percent of genes are conserved between

Answer 50

the fruit fly and humans - The two organisms appear to share a core set of genes

Question 51

When Scientists inserted human gene associated with early-onset Parkinson's disease into fruit flies

Answer 51

they displayed symptoms similar to those seen in humans with the disorder. -Thus control of expression of this gene may be similar between the 2 organisms raising the possibility that Drosophila could act as a new model for testing therapies aimed at Parkinson's.

Question 52

Researchers have compared the human genome with the genomes of the

Answer 52

chimpanzee, mouse, rat, and other mammals. - Identifying the genes shared by these species but not by non- mammals provides clues about what it takes to make a mammal. - Identifying the genes shared by chimpanzees and humans but not by rodents gives information about primates.

Question 53

In single-base substitutions, chimp and human genomes differ by only

Answer 53

1.2%

Question 54

chimps &humans: | Longer stretches of DNA show a ___% difference due to

Answer 54

2.7% insertions or deletions of larger regions in the genome of one or the other species. – Many of the insertions are duplications or other repetitive DNA.

Question 55

A __ of the human duplications are not present in the chimpanzee genome and some contain regions associated with human diseases.

Answer 55

third - Transcription factors regulate gene expression and thus play a key role in orchestrating the overall genetic program.