Bioinformatics and Functional Genomics, 2nd Edition

Chapter 18: Eukaryotic Genomes

This page offers web documents and resources that are referred to in Chapter 18. Figure 18.1 presents a tree by Baldauf et al. showing the relationships of the eukaryotes, and in the chapter we follow this tree from bottom up. Topics include the protozoans (Trichomonas, Giardia); unicellular pathogens (trypanosomes and Leishmania); the Chromalveolates (the malaria parasite P. falciparum and other apicomplexans; the ciliophora Paramecium and Tetrahymena; nucleomorphs; Stramenopiles such as diatoms); the plants; and slime molds. When we arrive at the metazoans (animals) we divide these into the great groups of nematodes (such as the worm C. elegans), insects (e.g. fruitfly, mosquito, honeybee), and chordates (Ciona). We conclude with descriptions of fish (diverged from humans about 450 million years ago [MYA]), chickens (310 MYA), opposum (180 MYA), mammals from dog to cow (100 MYA), rodents (80 MYA), and primates (50-5 MYA). For each organism we survey its genome, highting key properties, web resources, and bioinformatics problems.

Web documents
Page
Description
Web Document 18-1
758
metazoan (animal) kingdom superphyla and phyla
Web Document 18-2
758
phylum bilateria including the Coelomata (animals with a body cavity), Acoelomata (animals lacking a body cavity such as flatworms) and Pseudocoelomata (such as the roundworm C. elegans)
Web Document 18-3
778
Web resources for the study of the mouse and rat
Web Document 18-4
779
Primate lysozyme sequences used for phylogenetic analysis
Web Document 18-5
780
Primate resources
Web Document 18-6
782
256,157 bases of DNA from a eukaryotic genome in the fasta format


Chapter 18 Resources
Powerpoint of the eukaryotic genomes lecture from Genomics (November 23, 2009)
Course site for Genomics (260.605, 2nd quarter 2009-2010). This companion site includes information such as the class schedule and assignments.
Key URLs: NCBI BLAST page; UCSC