PEG10 (paternally expressed gene 10) is a paternally expressed gene (meaning only the paternal allele is expressed) that has an essential role in the formation of the placenta of the mouse. In the mouse genome, the PEG10 gene is flanked by the SGCE and PPP1R9A genes. To study the origin of PEG10, you examine syntenic regions spanning the SGCE and PPP1R9A loci in the genomes of several vertebrates, and you note that the PEG10 gene is present in the genomes of placental and marsupial mammals but not in the platypus, chicken, or fugu genomes.
The green bars in the figure indicate the exons of each gene. The gray bars represent LINEs and SINEs, and the blue bars represent long terminal repeat (LTR) elements of retrotransposons. Solid black diagonal lines link introns, and dashed black lines connect orthologous exons. Arrowheads indicate the direction of transcription.
Using the predicted protein sequence of PEG10, you perform a tblastn search for homologous genes and find that the most similar sequences are in a class of retrotransposons (the sushi-ichi retrotransposons). Propose an evolutionary scenario for the origin of the PEG10 gene, and relate its origin to its biological function.

Yeager, M., et al. [(2007) Nature Genetics 39:645–649] and Sladek, R., et al. [(2007) Nature 445:881–885] have used single-nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS) to identify novel risk loci for prostate cancer and Type 2 diabetes, respectively. Each study suggests that disease-risk genes can be identified that significantly contribute to the disease state. Given your understanding of such complex diseases, what would you determine as reasonable factors to consider when interpreting the results of GWAS?

You are studying similarities and differences in how organisms respond to high salt concentrations and high temperatures. You begin your investigation by using microarrays to compare gene expression patterns of S. cerevisiae in normal growth conditions, in high salt concentrations, and at high temperatures. The results are shown here, with the values of red and green representing the extent of increase and decrease, respectively, of expression for genes a–s in the experimental conditions versus the control (normal growth) conditions. What is the first step you will take to analyze your data?

Dominguez et al. (2004) suggest that by studying genes that determine growth and tissue specification in the eye of Drosophila, much can be learned about human eye development.

What evidence indicates that the eyeless gene is part of a developmental network?

Dominguez et al. (2004) suggest that by studying genes that determine growth and tissue specification in the eye of Drosophila, much can be learned about human eye development.

What evidence suggests that genetic eye determinants in Drosophila are also found in humans? Include a discussion of orthologous genes in your answer.

Two similar genes that arose from a gene duplication and are found in the same organism are called what?

Synteny describes conservation of what?

The genetic difference between two Drosophila species, D. heteroneura and D. silvestris, as measured by nucleotide diversity, is about 1.8 percent. The difference between chimpanzees (Pan troglodytes) and humans (H. sapiens) is about the same, yet the latter species is classified in a different genera. In your opinion, is this valid? Explain why.

How do comparisons between genomes of related species help refine gene annotation?