Introducing Genomes

Dr Louise Johnson
l.j.johnson@reading.ac.uk
What’s a genome and why sequence it?
Some terminology

Eukaryotic
chromosome:
can be sex
chromosome,
or autosome Prokaryotic “chromosome” –
typically circular, more gene-
dense and much smaller
Sex chromosomes
More terminology

• Karyotype = number of chromosomes in a cell

• Ploidy is the number of sets (2 = diploid)
• Aneuploidy = wrong number of chromosomes
Organelle genomes

Mitochondrial genomes are

approx. 10-15kB, Chloroplast
genomes are larger, approx.
100-200kB.
Different types of chromosomes are inherited
differently
• Autosomal genes
• Y-linked genes
• X-linked genes
• Mitochondrial genes
• Genes of our microbiome?
Genome sizes: make a diagram for your notes

Chloroplasts

Mitochondria
100bp 1Kb 10Kb 100Kb 1Mb 10Mb 100Mb 1Gb 10Gb 100Gb 1Tb

Genome Sizes (log scale)

 Viruses and giant viruses
SARS-
CoV-2
30kB

Circoviridae
1-2Kb

Giant viruses 3MB

Prokaryotes
• Generally compact, circular genomes
• Genes arranged into operons
• Plasmids as “optional extras”

Nasuia deltocephalinicola Scytonema hofmanni

112kB 12MB
Eukaryotes
• Typically large genome (up to
150Gb; but Encephalitozoon
cuniculi 2.9 MB )
• Organised into chromosomes (1 to
1600; usually 10-100)
• Organelles – mitochondria,
plastids such as chloroplasts – can
have genomes separate from the
nuclear genome.
Protists are just plain weird
Polychaos dubium – 670 Gb genome?
Paramecium – two types of cell nucleus
Metagenomes
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How to find genes?
• Predicted ORFs
• Homology
• CpG islands
• RNA sequencing (transcriptome) 19
Current state of the genome
• Just over 3 billion base pairs (haploid)
• 875 gaps in the sequence, some substantial (eg centromeric
heterochromatin) NO GAPS AS OF 1st APRIL 2022
• Less than 1 error per 100Kb
• 19,969 protein coding genes (600 fewer than last year’s predictiona)

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Variation within humans

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40 million differences between the human and
chimp genomes: 35M substitutions, 5M indels
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