Genome Structure and Chromosomes

Haplodiploidy and Chromosome Types

• Bees, wasps, and ants are haplodiploid, with haploid males and diploid females.
• Different types of chromosomes are inherited differently: autosomal genes, Y-linked genes, X-linked genes, and mitochondrial genes.

Mitochondrial Eve

• Mitochondrial Eve was not the first woman, nor was she the only woman alive at the time, nor was she the only woman who left descendants.
• She was just our last common ancestor if you only consider the female line.

Viroids

• Viroids are small RNA molecules that do not code for any proteins but use the host's RNA polymerase to replicate themselves.
• The smallest known pathogen is the coconut cadang-cadang viroid, which is a 246bp RNA molecule that kills 1 million trees a year.

Viruses and Giant Viruses

• Viral genomes tend to be compact.
• Genes in viruses often overlap and are multifunctional.
• Typical virus genome sizes are in the tens of thousands of base pairs, but there are extremes: single-stranded DNA viruses can be less than 2Kb in length, and 3Mb Pandoraviruses, discovered in 2013, infect amoebas.

Prokaryotes

• Prokaryotes have generally compact, circular genomes.
• Genes are arranged into operons.
• Plasmids are 'optional extras'.
• There are extremes: N. deltocephalinicola has the smallest prokaryotic genome at 112Kb, and S. hofmanni has the largest prokaryotic genome at 12Mb.

Eukaryotes

• Eukaryotes have typically large genomes organized into chromosomes.
• Organelles like mitochondria and chloroplasts can have genomes separate from the nuclear genome.
• Nobody has much of an idea what causes evolution/variation in chromosome number; it's an unsolved mystery.
• Within mammals, one of the monkeys has the most chromosomes at 97, and the muntjac deer has the fewest at 4.

Protists

• Protists are an extremely diverse group of unicellular eukaryotes.
• Some protists, like Paramecium, have two kinds of cell nuclei: one 'working memory' (macronucleus) containing many thousands of tiny, gene-sized 'chromosomes', and one 'master copy' micro nucleus containing the germline genome.

Human Genomes

• Humans are a terrible model organism due to long generation time, small litter sizes, and huge ethical problems with experimentation.
• The understanding of the human genome has been pieced together from various sources, including pedigrees and other genomes.

Gene Numbers

• In bacteria, identifying genes is relatively straightforward.
• In humans, it's not, because genes are hidden among a lot more junk.
• There are also large introns, splice sites, and alternative splicing patterns.
• ORFs can be found bioinformatically, but a very short ORF is unlikely to be transcribed.
• Homology with known genes from other species can also be used to help find genes.

Chromosome Structure

• Eukaryotic chromosome can be a sex chromosome or an autosome.
• Prokaryotic chromosome is typically circular, more gene-dense, and much smaller.
• One way the genome can be structured is that there can be sex chromosomes, which are subject to very different evolutionary pressures from autosomes.

Sex Determination

• XY systems like mammals have are not the only way to do it.
• Platypuses have ten sex chromosomes, and birds have a WZ system, as do moths.
• Some spiders have an X1X20 system with males heterogametic, and nematodes have an XO system where the female has more chromosomes than the male.
• Sex chromosomes aren't the only way to do sex determination; clownfish start male and turn female when they come to dominate a group, and alligators and crocodiles have temperature-dependent sex determination.