New Genes Flashcards
(14 cards)
Describe sequence homology
Uncovers evolutionary connections through shared ancestry in biological sequences
- Homologue, common origin
- Orthologue, speciation event
- Paralogue, duplication event
Describe gene duplication as a driver of biological diversity
Gene duplication provides raw material for evolutionary change without compromising original gene fuction.
Proposed by susumu Ohno
- Ohnologue, specific subset of paralogyes but originates from whole genome duplication, which duplicates the entire genome rathre than individual genes
Describe whole-genome duplication
wgd drives innovation by providing raw material for fuctional diversification, leading to new gene functions, complex traits, and increased organismal complexity
What are the possible fates of duplicated genes?
Neofunctionalisation: one copy evolves a new function
Subfunctionalisation: both copies share the ancestral function
Gene conservation: both copies retain the same function
Nonfunctionalism: one copy becomes a psuedogene
Describe gene duplication and the orthologye conjecture
Orthologues typically retain sequence, structure and function similariy. Paralogues can follow diverse fates
- Orthologue conjecture support: w values are more similar in lineages from speciation events than in those from duplication events
- Neofunctionalism trend: duplication often leads to increased w in one paralogue, driving evolution of novel gene functions
Describe fish antifreeze proteins
Glycoproteins and small protiens. Two major types
- antifreeze glycoproeins (AFGPs) found in antarctic notothenioid fishes and northern cod fishes and three other structurally unique small antifreeze proteins in unrelated taxa.
Describe the escape from adaptive conflict model
Suggests gene duplication resolves adaptive conflict by allowing optimisation of separate functions in duplicates
- in antarctic zoarcid fish, sialic acid synthase gene with duel SAS and ice-bindig functions duplicated. one evolved into a type III antifreeze protein by removing structural conflict, allowing rapid optimisation for freezing point depression
Describe human globin family
Subfunctionalisation
Alpha and beta globins arose from an ancestral gene duplication. Original functions split.
Describe transposable elements
Facilitate exon shuffling, gene duplication and regulatory element creation.
Genome reshaping: genome structure and size by promoting chromosomal rearrangements, insertions and deletions
Functional gene evolution: RAG1 and 2 for vertebrate adaptive immunity.
Also contribute to new promoters, enhancers and microRNAs
Describe ostreococcus tauri
Minimal algae: smallest free-living eukaryote with 1 mitochondrion and one chloroplast
Streamlined genome. Ubiquitous lineage of marine pico-algae
Describe the role of outlier regions in algal genome innovation
- Insulation: the BOC region is insulated from the rest of the chromatin
-Transcriptoics: increased gene expression in the outlier region - Methylation: lower gene silencing
-TEs: localised in outlier regions - Regulatory networks: can be expanded by TEs
- Domain shuffling: TEs facilitte the rearrangement and duplication of PKS gene domains
Describe horizontal gene transfers
Transformation (uptake of free DNA), transduction (phage mediated transfer) and conjugation (plasmid exchange)
Introduces new genes and fnctions. Or acquisition of photosythetic genes in algae.
Describe the viral legacy in our genomes
- LTR and retroviral protein co-option: Long Terminal Repeats (LTRs) and retroviral genes
are repurposed by host genomes, contributing to gene regulation and novel functions. - Syncytin origin: syncytin-1 is derived from an endogenous retroviral envelope (env) gene
and is essential for placental development by promoting syncytiotrophoblast cell-cell fusion. - Evolutionary innovation: Retroviral co-option exemplifies how ancient viral sequences drive
evolutionary adaptation in mammalian reproduction.
HERV expression: analysed expression of human endogenous retroviruses (HERVs) across
13,000 samples from 54 normal tissues, identifying transcripts in all tissues.
* LTR-driven transcription: identified 9 proviruses with LTR-driven transcription, biased by
tissue type, with older proviruses showing higher expression.
* Functional insights: some proviruses retain intact ORFs (e.g., gag), suggesting potential
protein expression in almost every tissue measured. Biological sex influenced expression in
one tissue, while age and death timing had minimal impact.
Describe vAMT
Viral ammonium transporter in Ostreococcus
- Minimal alga: smallest free-living eukaryote (~0.8 micron, 1 mitochondrion, 1 chloroplast)
- Giant viruses: Ostreococcus is infected by large dsDNA viruses (OtVs; Phycodnaviridae).
- vAMT: the genome of OtV-6 harbours a gene coding for a putative ammonium transporter.
- Host-virus HGT: vAmt is host-derived, conserved and was acquired via HGT.
- Viral tinkering: OtV6 infections amend Ostreococcus ammonium uptake.
