Week 5 The ‘Omic’ Era Flashcards
What the difference between genomics and transcriptomics?
Genomics is the study of genes, whilst transcriptomics is the genes expressed
What are the four steps in whole-genome sequencing and analyses?
- Shotgun sequencing
- Sequence alignment and assembly
- Translation and gene annotation
- Prediction of metabolic pathways
What are the four steps of shotgun sequencing?
- Entire genome is digested into many small fragments
- Small fragments are then cloned into arterial artificial chromosomes (BAC)
- Sequencing
- Computers analyse the sequence data for overlapping regions to form several large contigs
What might you do if you have gaps in your contigs in shotgun sequencing?
Can bridge the gap by designing primers
How do you obtain a genome form shotgun sequencing?
Via the alignment of many sequences
After alignment what do you do?
Translate to amino acids
How do you know the gene sequence as you can start at 1, 2 or 3 and get different amino acid sequences?
You read the three for forwards and reverse and observe the stop codons to observe which reading frame has the least amount of disruption
In genomics, how will you know what your sequences function is?
You compare the sequence nucleotides/amino acids/proteins against a database like blast to see which protein your gene might be coding for
How do you find metabolic pathways in a metabolic reconstruction procedure?
By looking at multiple genes and searching databases of metabolic pathways
What is this an image of and what can it be used for?
The Kyoto encyclopaedia of genes and genomes, used for comparing genes in pathways
Can Prochlorococccus perform CO2 fixation?
Yes, it has all the nessecary genes
What does this image show
That the purifying selection of prochorococcus means that the high light strain has lost its nitrate utilisation capability
What are metagenomics?
Genomic sequencing of a ‘community’ of mixed individuals/populations
Is culturing required for metagenomics?
No
What are Lokiarchaetoa?
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
What are these?
The Asgard archea which carry a lot of Eukaryotic signatures
What did Davies et al. Discover about the transcriptomic responses in carribean coral when exposed to thermal and OA stress?
That there was a suppression in genes responding to environmental stimuli
What are the advantages of transcriptomics?
- High resolution
2. Information on precisely which genes are up/down regulated
what are the disadvantages of transcriptomics?
- Also critical to know the life and moult stage, reproductive cycle and disease status
- There are noisy data sets which require more robust techniques such as RT-qPCR
What is transcriptomics, what has allowed it and what does it measure?
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
What did Mason et al. 2012 find out about oil spills and oceanspirillales using transcriptomics?
That cells possessed the genes coding for alkane and cycloalkane breakdown
Why would we need single cell analysis?
Eliminate the need to search and bin the many sequenced fragments and it can provide direct links amount different genes
What does DNA tell us in genomics?
The gene potential
What does mRNA tell use in transcriptomics?
Which genes are being actively expressed
