BIO314 molec ecol - GMOs

what was the first prokaryotic genome that was sequenced?

-bacteriophage (an RNA genome)

-took multiple years

-codes for only 4 proteins

what was the first eukaryotic genome that was sequenced?

-yeast was first sequenced

-c. elegans was two years later

_____ DNA is difficult to sequence.

-repetitive

-sanger sequencing was better at it

what is important to remember when sequencing new organisms?

-depth versus breath (not enough money for method that includes BOTH, must choose between depth and breath)

-analysis and storage of information is often more costly that the actual physical work

what are the 3 stages of sequencing?

-primary = done by the machine

–secondary = filtering raw reads, quality assurance

–tertiary analysis = processing multiple samples, make biological sense of the reads

what is commonly seen when sequencing non-model organisms?

-tend to have bias towards vertebrates and in particular mammals (things we already know and love)

-tend to be microbiomes (where human health is currently focused!)

-reflect phylogenetic history

what comprises comparative genomics?

-gene content, gene order, regulatory sequences, non-coding sequences, other structural landmarks

-genome functioning, similarities, differences, evolutionary history and the process

what are orthologous structures?

-diverged after speciation event

what are paralogous structures?

-diverged after a duplication event

comparing non-model and model organisms

-comparison to known and unknown often is a place to start (you have genome from a known species compared to an unknown species)

-a place to start for testing speciation hypotheses

-also for evolutionary history and even conservation practices (panthera family)

what are the molecular adaptations of the panthera family?

-carnivorous diet

-muscle strength

-coat color

-oxygen use

what is an example of gene expression in heliconius butterflies?

-batesian (1 poisonous, 1 not) and mullerian (both poisonous) mimicry studies

-3 genomic regions for most wing patterns

-transcriptional factors determine most of the differences

what is an example of gene expression in peppered moths?

-an insert of 22,000bp into the same gene in heliconius that deals with wing patterns

-molecular clock confirms

what are the different types of genomics?

-evolutionary genomics (ex: when did vertebrates come on to land)

-population genomics

-landscape genomics (ex: phylogenomics. without NGS this wouldn’t happen)

-speciation

-conservation genomics

what is the relationship between giant pandas and other bears?

-giant pandas are true bears (family ursidae)

–they are not closely related to red pandas (ailuridae, a completely different family)

-genomic data strongly support a split between pandas and the rest of bears about ~12–20 million years ago

-no major digestive-enzyme gene gains for plant digestion

-still have a carnivorous digestive system

-their bamboo diet appears tied to a loss of umami taste receptor gene (T1R1) → reduced taste for meat

what are panda population structures shaped by?

-mountain range isolation in china (habitat fragmentation)

what is the qinling panda population?

-lives exclusively in the qinling Mountains

-exhibits distinct morphology (brown-tan coat, smaller skull, different cranium shape)

what is the sichuan panda population?

-occupies several mountain ranges in sichuan province

-more genetically diverse and includes most surviving pandas

what is transcriptomics?

-genome expression in various habitats

what is proteomics?

-determines how we get proteins and their structure

what is metabolomics?

-expression of metabolites (hormones, signaling molecules)

___________ is another way we have gene expression aside from genes turned on/off.

epigenetics

what is genome editing?

-synthesize and edit large portions of the genome

-GMOs, crisper/cas9

what are GMOs?

-one or more genes from a different organism have been introduced into their DNA via molecular biology

-a plasmid is introduced into agrobacterium with the gene and a promoter

–agrobacterium is then used to infect the plant

–may take a few tries to be heritable

-several perceived risks

–human health

–genetic pollution

what is the history of GMOs?

-technique has been around since the 1970's but then they started using it with E. coli

-people were worried about cancerous cells and what if they are ingested?

-first field trial = 1986, between 1987-1990 there were 90 trials

-1991 = 171 applications

-1998 = 15000 field trials

what is an alternative to GMOs?

-current techniques use mutagens to generate new varieties

-over 2000 available

-don't face the same critique as GMO's

what are the concerns with utilizing GMOs?

-will GMO's spread beyond their release sites and outcompete wild types?

-will the genes spread to new hosts?

-will the introduced genes affect species that interact with the GMO's?

-how were/will these be substantiated? (gene tracking, phylogeography)

what is gene tracking?

-horizontal gene transfer (between bacteria or other organisms, NOT transfer from parent to child)

-conjugation = F plasmids

-transformation = free DNA

-transduction = virus (when viruses leave pieces of DNA in infected organism)

what are the effects of GMOs on communities?

-new genes do not confer an advantage (per rhizome studies)

-vertical transmission results in cross fertilization

-questions to ask: what does this mean for the plant? how can we test it? how do these genes affect the species that feed on them? non-target species?

what future technology could be developed for GMOs?

-accessibility of markers for any organism (if you are making a GMO organism you want a marker to go with it so you can track the organism)

-fewer technical limitations

-faster laboratory analyses

-data storage and analysis more challenging

-impliment use of AI

what is the crisper/cas9 method?

-RNA defense system for bacteria against viruses to silence invading DNA

-basically a way to stick a gene into ANY genome and get a reasonable number of cells

-initially used to take out genes but now used to insert genes

how has the crisper/cas9 method been used in mosquitos?

-transgenic mosquitos carrying anti-pathogen effector genes targeting human malaria parasites, denge and Zika

-reduces risk of mosquito-borne illnesses