Week 5 The ‘Omic’ Era

Question 1

What the difference between genomics and transcriptomics?

Answer 1

Genomics is the study of genes, whilst transcriptomics is the genes expressed

Question 2

What are the four steps in whole-genome sequencing and analyses?

Answer 2

1. Shotgun sequencing
2. Sequence alignment and assembly
3. Translation and gene annotation
4. Prediction of metabolic pathways

Question 3

What are the four steps of shotgun sequencing?

Answer 3

1. Entire genome is digested into many small fragments
2. Small fragments are then cloned into arterial artificial chromosomes (BAC)
3. Sequencing
4. Computers analyse the sequence data for overlapping regions to form several large contigs

Question 4

What might you do if you have gaps in your contigs in shotgun sequencing?

Answer 4

Can bridge the gap by designing primers

Question 5

How do you obtain a genome form shotgun sequencing?

Answer 5

Via the alignment of many sequences

Question 6

After alignment what do you do?

Answer 6

Translate to amino acids

Question 7

How do you know the gene sequence as you can start at 1, 2 or 3 and get different amino acid sequences?

Answer 7

You read the three for forwards and reverse and observe the stop codons to observe which reading frame has the least amount of disruption

Question 8

In genomics, how will you know what your sequences function is?

Answer 8

You compare the sequence nucleotides/amino acids/proteins against a database like blast to see which protein your gene might be coding for

Question 9

How do you find metabolic pathways in a metabolic reconstruction procedure?

Answer 9

By looking at multiple genes and searching databases of metabolic pathways

Question 10

What is this an image of and what can it be used for?

Answer 10

The Kyoto encyclopaedia of genes and genomes, used for comparing genes in pathways

Question 11

Can Prochlorococccus perform CO2 fixation?

Answer 11

Yes, it has all the nessecary genes

Question 12

What does this image show

Answer 12

That the purifying selection of prochorococcus means that the high light strain has lost its nitrate utilisation capability

Question 13

What are metagenomics?

Answer 13

Genomic sequencing of a ‘community’ of mixed individuals/populations

Question 14

Is culturing required for metagenomics?

Answer 14

No

Question 15

What are Lokiarchaetoa?

Answer 15

An archea that forms a monophyletic group with Eukaryotes, encoding a repertoire of eukaryotic signature proteins, with provides strong support for the hypotheses that the eukaryotic host evolved from a archdeacon

Question 16

What are these?

Answer 16

The Asgard archea which carry a lot of Eukaryotic signatures

Question 17

What did Davies et al. Discover about the transcriptomic responses in carribean coral when exposed to thermal and OA stress?

Answer 17

That there was a suppression in genes responding to environmental stimuli

Question 18

What are the advantages of transcriptomics?

Answer 18

1. High resolution

2. Information on precisely which genes are up/down regulated

Question 19

what are the disadvantages of transcriptomics?

Answer 19

1. Also critical to know the life and moult stage, reproductive cycle and disease status
2. There are noisy data sets which require more robust techniques such as RT-qPCR

Question 20

What is transcriptomics, what has allowed it and what does it measure?

Answer 20

It is the study of gene expression in a community and has been established via NGS sequencing and it measures the RNA profile in a mixed community to understand the processes and pathways that are active

Question 21

What did Mason et al. 2012 find out about oil spills and oceanspirillales using transcriptomics?

Answer 21

That cells possessed the genes coding for alkane and cycloalkane breakdown

Question 22

Why would we need single cell analysis?

Answer 22

Eliminate the need to search and bin the many sequenced fragments and it can provide direct links amount different genes

Question 23

What does DNA tell us in genomics?

Answer 23

The gene potential

Question 24

What does mRNA tell use in transcriptomics?

Answer 24

Which genes are being actively expressed