Lecture #10 - Marine Genomics Flashcards
genome
all the DNA on all of the chromosomes in the nucleus OR in mitochondria (chloroplasts for plants)
what do most cells have?
2 genomes: nuclear and mitochondrial
Nuclear genome
tens of thousands of protein coding genes
Mitochondrial genome
13 protein coding genes; no recombination because only maternally inherited
What makes a good genetic model?
Smaller genomes, less complex, potential for a lot of offspring, easier to study
what is the average genome size?
1.5 billion bp
is the size of the genome related to organismal evolutionary placement?
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
gene
DNA at a specific location on a chromosome that has a function
3 types of genes
protein coding, RNA specifying, untranscribed
Protein coding
mRNA that is translated into an enzyme, receptor, hormone, or structural protein
RNA specifying
encodes a specific RNA (microRNAs, tRNAs, rRNAs)
Untranscribed
regulatory element, chromosomal structural element, or origin of replication
locus
a gene’s position on a chromosome
alleles
pairs of genes that code for the same function at the same locus
exons
portions of RNA that form message mRNA and include the protein coding regions; forms mRNA
introns
portions of RNA that are removed or spliced out; typically much bigger than exons; splice out of RNA to form mRNA
NGS
next generation sequencing
what does NGS do?
produces hundreds of millions of short sequences (50 - 175 bp), billions of nucleotides
Produces many short sequences as opposed to a few long sequences
Exome sequencing
sequencing just the exons (not the non-coding intron) of protein coding genes; NOT the whole genome
Transcriptome sequencing
represent fewer genes than the entire exome, but one gene can be expressed many times; starts w/ mRNA, sequencing expressed mRNA genes
Genotyping by sequencing (GBS)
a way to “sample” the same, small part of genome in many individuals
SNP
single nucleotide polymorphism
what is an SNP?
genetic variation, difference among individuals or populations
what does population genomics tell us?
Population parameters
Local adaptation
Population origin
why do we care about population genomics?
Population connectivity
MPAs
Illegal fishing
Coalescences
the process of tracing the ancestral lineages of gene copies back in time until they converge at a common ancestor, forming a genealogical tree
speed of coalescence is a function of
population size
