BME 130 – Genomes Lecture 8 Genome Anatomies

(Black Death) genome sequenced Genomics in the news Yersinia pestis (Black Death) genome sequenced Johannes Krause http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10549.html http://www.nytimes.com/2011/10/13/science/13plague.htm

Exon and Intron length distribution in the human genome

Nucleosomes: beads on a string

More condensed: 30 nm fiber

Yeast centromere

Yeast kinetochore

Human kinetochore

Telomeric repeats

Gene Density on chr1 of Arabidopsis Human chr1

This “region” in current human genome assembly (hg19)

Genome sizes

Table 7.2 Genomes 3 (© Garland Science 2007)

http://www.ncbi.nlm.nih.gov/homologene 26,887 17,959 22,165 Table 7.4 Genomes 3 (© Garland Science 2007)

Figure 7.16 Genomes 3 (© Garland Science 2007)

Figure 7.17 Genomes 3 (© Garland Science 2007)

Table 7.5 Genomes 3 (© Garland Science 2007)

Figure 7.18 Genomes 3 (© Garland Science 2007)

Gene families Figure 7.19 Genomes 3 (© Garland Science 2007)

Figure 7.20 Genomes 3 (© Garland Science 2007)

Figure 7.21 Genomes 3 (© Garland Science 2007)

Figure 7.22 Genomes 3 (© Garland Science 2007)

Figure 7.23 Genomes 3 (© Garland Science 2007)

Figure 7.24 Genomes 3 (© Garland Science 2007)

Prokaryotic Genome Anatomies No nuclear envelope. Instead, a nucleoid

Genome can be naturally compacted by supercoiling it

Model for bacterial genome organization HU protein – binds DNA

Plasmid and extra-chromosomal elements complicate the question of what is the genome

Prokaryotic genomes are gene-dense

Absence of repeat sequence simplifies assembly From 384 assembled bacterial and archaeal genomes Kingsford et al. BMC Bioinformatics 2010 11:21   doi:10.1186/1471-2105-11-21

Gene organization in prokaryotic genomes

An operon from Aquifex aeolicus Glutamyl-tRNA aminotransferase C Recombinase protein Twitching mobility protein Cytidylate kinase Phosphotidylglycero-phosphate synthase

Genome sizes are proportional to the number of genes, but vary greatly

Different modes of life require radically different gene catalogs

Horizontal gene transfer is rampant So what is a species?

Eukaryotic organelle genomes

Human mitochondrial genome (mtDNA)

http://evolution.berkeley.edu

http://www.mitomap.org/WorldMigrations.pdf

Green et al., Cell 134(3):416 2008

Yeast mitochondrial genome (mtDNA)

Bacteriophages

Overlapping ORFs

Lytic infection

Figure 9.4b part 1 of 2 Genomes 3 (© Garland Science 2007)

Figure 9.4b part 2 of 2 Genomes 3 (© Garland Science 2007)

Lysogenic infection

Eukaryotic retrovirus structure

Retrovirus genome

Figure 9.16 Genomes 3 (© Garland Science 2007)

Drosophila phylogeny and P-elements