L2 Genomics

Question 1

Tree of life based on rRNA genes

Answer 1

Assert that all living things have a common ancestor

Question 2

Organelle Genomes

Answer 2

Eukaryotic cells contain a nuclear genome and organelle/plastid genomes

multiple “genomes” exist within a eukaryotic cell

Question 3

Eukaryotes vs Prokaryotes

Answer 3

See OneNote

Question 4

Size and structure of organelle DNA

Answer 4

• circular genomes

- genes for rRNA, tRNA, some proteins

Question 5

Origin of Eukaryotic cell

Answer 5

See OneNote

Endosymbiont Hypothesis

Question 6

rRNA comparisons - if endosymbiont

Answer 6

See OneNote

Question 7

rRNA comparison - if endogenous

Answer 7

See OneNote

Question 8

Comparative Genomics

Answer 8

study of the pattern of similarity and difference between genomes of different species

central concept:

• sequence homology, identity because it derived from a common ancestor
• infer process from pattern

Question 9

Human vs Mouse

Answer 9

See OneNote

- there is an excess of rearrangements in rodent lineages

Question 10

Karyotopic Evolution

Answer 10

See OneNoten diagram

• chromosome number changes e.g. chimps have one more chromosome than humans

Short repeats = telomeres
Telomere in the middle of the chromosome arm indicates that the telomere there was once active

Question 11

Metagenomic

Answer 11

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

Can now sample genomes that are not culturable in the lab

Question 12

Phylogenomics

Answer 12

Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics.

How organisms are related to each other at the genomic level

Question 13

Evolutionary genomics applications

Answer 13

• metagenomics
• phylogenomics
• non-model => new-model organisms
• functional genomics
• population genomics
• trait mapping

Question 14

Dideoxy Sequencing

Answer 14

See OneNote

- Fred Sanger

Question 15

The first sequencing of the human genome

Answer 15

See OneNote

• dideoxy sequencing
  1. automated calling with dyes
  2. high-resolution traces
  3. Solexa’s: reversible terminator chemistry

Question 16

Solexa

Answer 16

See OneNote Solexa page

Question 17

Barcodes

Answer 17

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s DNA to identify it as belonging to a particular species.[1] It differs from molecular phylogeny in that the main goal is not to determine patterns of relationship but to identify an unknown sample in terms of a preexisting classification.[2] Although barcodes are sometimes used in an effort to identify unknown species or assess whether species should be combined or separated

Question 18

Indexing

Answer 18

To distinguish between the clusters and thereby allow correct paired end assignments

Question 19

Paired end

Answer 19

See OneNote paired end page

Paired-end sequencing allows users to sequence both ends of a fragment and generate high-quality, alignable sequence data. Paired-end sequencing facilitates detection of genomic rearrangements and repetitive sequence elements, as well as gene fusions and novel transcripts.

Question 20

Mate pairs

Answer 20

See OneNote note and mate pair page

Question 21

Pyrosequencing

Answer 21

See OneNote page on Pyrosequencing

Sequencing by synthesis

Question 22

PacBio

Answer 22

Their custom dyes join not to the nucleotide but to the phosphate so the reaction works much more frequently as you don’t need to deblock, can get very long reads

Question 23

Nanopore sequencing

Answer 23

Sequencing can be done with a very small machine, able to take out into the environment