12.1

Question 1

what is shotgun sequencing?

Answer 1

genomic DNA is sheared into short sequences and sequenced by next gen
assembler software looks for overlaps to assemble them into contigs

Question 2

what is the issue with shotgun sequencing?

Answer 2

has issues with repetitive sequences (nanopore helps with this)

Question 3

what are the advantages of long reads?

Answer 3

help with assembly and alignment of short reads

Question 4

what is read or sequencing depth?

Answer 4

number of times a base is represented within all the reads from a sequencing run
gives greater confidence

Question 5

what is a good sequencing depth?

Answer 5

> 100 for a new genome

Question 6

what is the math of sequencing depth?

Answer 6

average number of times one spot is sequenced

Question 7

what is genome assembly?

Answer 7

next gen and 3rd gen sequencing of all chromosomes

Question 8

what is transcriptomics?

Answer 8

next gen sequencing of all mRNA transcripts

Question 9

what is species identification?

Answer 9

sanger sequencing of one gene
COI (mtDNA) for animals
16srDNA for microbes
nucleur rDNA for fungi
cpDNA for plants

Question 10

what is evolutionary relationships anaylsis?

Answer 10

sanger and next gen sequencing of whole genome

Question 11

what is microbial ecology?

Answer 11

next gen sequencing of 16srDNA (for microbes)

Question 12

what is environmental DNA?

Answer 12

next gen sequencing of mtDNA

Question 13

why is mtDNA good for sequencing?

Answer 13

we have lots of copies of it and evolves at just the right rate

Question 14

who invented minisatellite DNA?

Answer 14

alec jeffries

Question 15

what are minisatellites?

Answer 15

small (10-100 bp sequences) that are repeated many times (up to 1000) in tandem arrays

Question 16

why are mini satellites important?

Answer 16

they have a ton of allelic variation due to mutations (slippage errors and unequal cross-over) that make them different in every person)

Question 17

what are microsatellites?

Answer 17

smaller minisatellites that can be amplified using pcr instead of southern blotting

Question 18

what are the other names for microsatellites?

Answer 18

STRs and SSRs

Question 19

how does microsatelite genotyping happen?

Answer 19

fluorescent primers are used to amplify
products are separated by electrophoresis
genotypes are identified by size of products

Question 20

what is multiplex analysis?

Answer 20

multiple microsatellites amplified at the same time using primers with different colours

Question 21

how do microsatellites cause genetic disorders?

Answer 21

involve trinucleotide repeats within genes
have versions with too many repeats

Question 22

what are examples of microsatellite genetics disorders?

Answer 22

huntington’s, myotyonic dystrophy, fragile X syndrome

Question 23

what is RFLP analysis?

Answer 23

restriction fragment length polymorphism analysis to detect them in gel electrophoresis

Question 24

what are RFLPs?

Answer 24

mutations that either create or destroy restriction endonuclease sites

Question 25

what are RFLPs caused by normally?

Answer 25

SNPs - single nucleotide polymorphisms

Question 26

what are SNPs caused by?

Answer 26

usually a single base mutation (most common genetic variation)

Question 27

what is a haplotype?

Answer 27

arbitrarily long stretch of DNA characterized by particular alleles at the SNP positions in the sequence

Question 28

what causes haplotypes?

Answer 28

SNPs that are close together and get inherited together

Question 29

what are SNP chips?

Answer 29

microarrays - use dna hybridization-based assay to determine genotypes at known SNPs

Question 30

what is GWAS?

Answer 30

genome wide association studies

Question 31

what is the point of GWAS?

Answer 31

looking for genetic links to diseases by looking for SNPs that are correlated with presence of disease