BIO 560: Seminar in Molecular Cell
Emiliania huxleyi Genome Annotation
Course Description
This course is aimed at students who desire to better understand how genes and other
features of genomes are predicted, and how to understand and make better use of the
vast amount of information flowing from genome projects. Genome annotation involves
obtaining biological information from unprocessed genomic DNA sequence data. It is a
process deciphering the landscape of genomic DNA and its key features. Hence, in this
course students, using the marine coccolithophorid Emiliania huxleyi as a model, will
learn about many of the searches, tools, and processes used to annotate, analyze and
compare eukaryotic genomes.
Student Learning Outcomes
1. become familiar with the Joint Genome Institutes eukaryotic annotation methods,
tools and computational pipeline for annotation,
2. be proficient at evaluating gene models, assigning gene names, describing gene
function, and recognizing unusual features pertaining to gene structure
3. develop knowledge of fundamental metabolic pathways, structures, and systems
characteristic of the biology and evolution of Emiliania huxleyi
4. gain stronger bioinformatics skills relating to gene prediction, sequence similaritybased searches, evidence evaluation, phylogenetic analysis, protein domain and
motif searchs, and Gene Ontology
5. have acquired stronger critical thinking, reasoning, and problem-solving skills,
scientific attitudes and values
6. appreciate the power of genome sequence information
Course Requirements:
Students will work in pairs and use manual annotation tools and processes to annotate
eukaryotic genes and proteins specific to Emiliania huxleyi. Grades will be based on
total accumulated points (250 total):
Gene Annotated (target=50 genes at 5 points each)
(2) Oral presentations (15 min)
Written report (3-5 pages)
Participation
250 points
50 points
50 points
50 points
Grades will be assigned on a straight percentage basis whereby:
90-100
A
80-89
B
70-79
C
60-69
D
< 60
F
August 26
September 1
September 8
September 15
September 22
September 29
Introduction to JGI’s Genome Sequencing
E. huxleyi Genome Portal
Annotation Guidelines
In Class Annotation
In Class Annotation
In Class Annotation
October 6
October 13
October 20
October 27
November 4
November 11
November 18
November 25
December 2
December 9
In Class Annotation
Oral Presentation #1
In Class Annotation
In Class Annotation
In Class Annotation
In Class Annotation
In Class Annotation
In Class Annotation
In Class Annotation
Oral Presentation #2/Written Report
Suggested Annotation Topics:
RNAi pathway
Urea Cycle
C4 Metabolism
Purine and Pyrimidine Biosynthesis
Amino Acid Biosynthesis
Nitrogen Metabolism
Gluconeogenesis
Glycolysis and the Oxidative Pentose Phosphate Pathway
Krebs Cycle
Transcription Factor Families
Alternative Oxidation Pathways (uncoupling proteins, NADH type II dehydrogenase,
alternative odidase)
Selenoproteins
Sulfur Metabolism
Phenylpropanoid pathway (phenyl ammonium lyase PAL)
Alkaloid Biosynthesis (amino acid decarboxylases)
Isoprenoid Biosynthesis
Cycolphillins
Useful Websites:
www.csusm.edu/EhuxGenome
http://expasy.org/tools/
http://genome.jgi-psf.org/Emihu1/Emihu1.home.html