Lecture #10 - Marine Genomics

Question 1

genome

Answer 1

all the DNA on all of the chromosomes in the nucleus OR in mitochondria (chloroplasts for plants)

Question 2

what do most cells have?

Answer 2

2 genomes: nuclear and mitochondrial

Question 3

Nuclear genome

Answer 3

tens of thousands of protein coding genes

Question 4

Mitochondrial genome

Answer 4

13 protein coding genes; no recombination because only maternally inherited

Question 5

What makes a good genetic model?

Answer 5

Smaller genomes, less complex, potential for a lot of offspring, easier to study

Question 6

what is the average genome size?

Answer 6

1.5 billion bp

Question 7

is the size of the genome related to organismal evolutionary placement?

Answer 7

NO, among plants and animals, the size of the genome is NOT related to organismal evolutionary placement

mammals have a smaller genome than amphibians and birds, which have smaller genomes than sharks

Question 8

gene

Answer 8

DNA at a specific location on a chromosome that has a function

Question 9

3 types of genes

Answer 9

protein coding, RNA specifying, untranscribed

Question 10

Protein coding DNA

Answer 10

mRNA that is translated into an enzyme, receptor, hormone, or structural protein

Question 11

RNA specifying

Answer 11

encodes a specific RNA (microRNAs, tRNAs, rRNAs)

Question 12

Untranscribed

Answer 12

not translated into mRNA; regulatory/chromosomal structural element, or origin of replication

Question 13

locus

Answer 13

a gene’s position on a chromosome

Question 14

alleles

Answer 14

pairs of genes that code for the same function at the same locus

Question 15

what are exons and what do they include?

Answer 15

portions of RNA that form mRNA; include the protein coding regions

Question 16

introns

Answer 16

portions of RNA that are removed or spliced out to form mRNA; typically much bigger than exons

Question 17

NGS

Answer 17

next generation sequencing

Question 18

what does NGS do?

Answer 18

produces hundreds of millions of short sequences (50 - 175 bp), billions of nucleotides
Produces many short sequences as opposed to a few long sequences

Question 19

Exome sequencing

Answer 19

sequencing just the exons (not the non-coding intron) of protein coding genes; NOT the whole genome

Question 20

Transcriptome sequencing

Answer 20

starts w/ mRNA, sequencing expressed mRNA genes

Question 21

Genotyping by sequencing (GBS)

Answer 21

a way to “sample” the same, small part of genome in many individuals

Question 22

SNP

Answer 22

single nucleotide polymorphism

Question 23

what is an SNP?

Answer 23

genetic variation, difference among individuals or populations

Question 24

what does population genomics tell us?

Answer 24

Population parameters
Local adaptation
Population origin

Question 25

why do we care about population genomics?

Answer 25

Population connectivity MPAs Illegal fishing

Question 26

Coalescences

Answer 26

traces the ancestral lineages of gene copies back in time until they converge at a common ancestor, forming a genealogical tree

Question 27

speed of coalescence is a function of

Answer 27

population size

Question 28

what does transcriptome sequencing allow?

Answer 28

one gene can be expressed many times

Question 29

Drawback of transcriptome sequencing

Answer 29

represent fewer genes than the entire exome