17/18 - Special Topics Flashcards
Describe the 16S marker gene
- Universal (in all prokaryotic organisms)
- Well conserved regions with robust primers
- Hyper variable regions give us enough information content to make phylogenetic trees
- Wide copy number variation is a problem (can artificially inflate perceived abundance)
- 16S is subjectible to horizontal gene transfer, though this is pretty rare.
- Evolutionary rate variation can make designing trees difficult
Name some commonly used gene markers that can be used for phylogeny (and other things)
- 16S rRNA
- Internal transcribed spacer (ITS, fungi)
- Mitochondrial genes
- recA (recombination and gene repair in bacteria)
- rpoB (RNA polymerase)
- amoA (ammonia monooxygenase)
How can we find novel gene markers?
What are some challenges with this method?
Use reference genomes and do an automatically scored search for genes which might be good.
Challenges:
- Developing a reasonable score
- Choosing data to search (one solution is to use only annotated protein coding genes from bacterial and archaeal genomes)
- Grouping all proteins in a set of diverse genomes is computationally intensive
What four properties were used to look at potentially new genetic markers?
- Universality (genomes gene is found in)
- Evenness (copy number): consistent copy number among organisms
- Monophyly (agreeing with preexisting taxonomies)
- Uniqueness (within family distance smaller than between family distance, pulling out ONLY gene of interest)
What are some limitations of the study that was looking for new gene markers?
- Limited to ref genomes
- Assumes taxonomic classifications are correct
- Reduced genomes had to be removed
- Analysis should be re-run on expanded set of genes (like non-protien coding genes)
- Equations have a bunch of unexplained constants
- A lot is known about current marker genes (eg. 16S)
In the mealybug example, where was gene transfer taking place?
Between tremblaya and moranella. No genes were transferred to the actual mealybug itself.
How does the blastocystis hominis resemble an organelle? How was this examined?
They have mitochondrion like characteristics (eg. cristae, DNA, transmembrane potential), but they have pathways more similar to hydrogenosomes (anaerobic derivates of mitochondria).
Examined with expressed sequence tags: Expressed Sequence Tags (ESTs) are essentially Sequence Tagged Sites (STS) that are represented in mRNA. They are derived as 300-500 bp single-pass mRNA sequence reads from many of the genes expressed in a given tissue and/or at a given developmental stage.
Looked at clusters encoding potential mitochondria and hydrogenosomal proteins.
They found 2 key enzymes involved in anaerobic energy metabolism.
It also has a mitochondria like genome with full length features, tRNAs and 2 NADH dehydrogenase subunits in ETC
There are also TIMs and TOMs
How is Nyctotherus ovalis similar to blastocystis hominis?
Also retained mitochondria proteins and an organellar genome, but lost similar components of the ETC.
Why is E chlorotica a good organism for studying lateral gene transfer?
It acquires plastids through feeding, conferring photosynthetic ability. These plastids do not divide, but provide energy and carbon to E chlorotica throughout its life span. Algae do not need to be present for plastid activity.
This sea slug acquired the gene psbO from algae V litorea
Describe the two conflicting results with lateral gene transfer in E chlorotica
Interdomain transfer of an algal gene to a mollusc, it’s expression in the foreign host and te gene being inserted into the germ line was observed by one study RT-PCR.
Significance: Gene transfer between distantly related species is possible!
Or not..
No evidence for algal derived HGT into the germ line of E chlorotica. This may be because algal DNA recovered using PCR indicated HGT that had gone undetected in second study or algal DNAs were integrated somewhere beyond eg genome (extrachromosomal form of DNA)
What is Amborella trichopoda?
A flowering plant (angiosperm) only found in new caledonia. It is a single living descendant of the common ancestor of all flowering plants
Why is it important to know the genome of amborella?
- As a reference for evolutionary studies
- To see how genes and gene families in flowering plants evolved
- Further our understanding of how flowering plants spread across the world.
What does whole genome analysis of amborella show?
That there are regions of synteny contianing homeologs (duplicated gene copies).
- Structural evidence of an ancient whole genome duplication event. This event predated angiosperm (flowering plant) diversification.
- Comparisons between amborella and other angiosperms made it possible to reconstruct the ancestral angiosperm gene content and gene order
- Amborella genome is a reference for understanding genome and gene family evolution throughout angiosperm history
What’s so special about tremblaya?
Smallest genome ever. Though the nucleus does not provide any genes!
Moranella is an endosymbiont of of tremblaya, but its genome is four times as large. Moranella is believed to bring in some genes that tremblaya lost.
The tremblaya genome reduction was driven by its own endosymbiont. The mealybug was able to function from tremblaya and moranella being able to make amino acids to supplement their sap diet.
