Metagenomics, functional genomics, and evolutionary genomics.
Supplemental Instruction
IowaStateUniversity / Leader: / Matt C.
Course: / Biol/Gen 313
Instructor: / Dr. Myers & Dr. Vollbrecht
Date: / 04/18/2017

Introduction: This worksheet discusses material covered in the thirty-fifthlecture(04/17/2017). Chapter 15examines these topics.

Concepts

  1. Metagenomics.
  2. Functional genomics.
  3. Comparative genomics.

Material

  1. Metagenomics of genomics.

In this section, we’ll briefly consider some important characteristics of metagenomics.

  1. What is a metagenome? How do we determine a metagenome?
  1. What could be one indicator that a eukaryotic organism like a protist was included in your metagenomic sample?
  1. As an extension of the above, you have one diploid protist with haploid number 5 and another diploid organism with a haploid number of four represent in your metagenome sample. What would this look like in the metagenomic data and how do you think conclusions from such data would differ from the actual?
  1. Functional genomics.

Here, we’ll consider some aspects of functional genomics.

  1. What are some reasons why transcriptome data and proteome data aren’t directly correlated?
  1. What does using a microarray accomplish?
  1. Briefly describe how a microarray works.
  1. How did the differential expression test described in class work?
  1. Evolutionary genomics.

At this point, we’ll discuss both homologous genes and the introduction to comparative genomics described in class.

  1. Cancer studies on an oncogenic src kinase in chickens initially gave concerns about a species leap for a chicken cancer-inducing virus to humans. This is because the human src kinase is fairly similar to the chicken src kinase. What is the term used to describe these similar genes?
  1. How would you expect genome homology to differ between comparison of two closely-related species and two more distantly-related species? Is this necessarily an absolute fact? Why?
  1. Consider three model organisms. E. coli, S. cerevisiae,and Mus musculus. Explain why for each question.
  1. Which of these likely has the smallest genome in base pairs?
  1. Which has the largest?
  1. Which has the highest ratio of genes to base pairs?
  1. Which pair will have the highest homology?

Things to do next

  • Focus your review on things that were difficult from this worksheet. If it was really challenging, don’t worry; these are meant to be tough and push your understanding of the topics we covered.
  • We’re back to definitions with most of this. I imagine the microarray will be the most complex for now, but focus on whatever is most problematic for you.
  • If you have any questions, ask me in session, in class, or by email. I’m more than happy to help.
  • Next session will be onThursday(04/20/2017) from 5:10 to 6:00 PM in Gilman 1051. We’ll cover material from Wednesday’s lecture.