15. Genomes and Genomics

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?

Annotation involves identifying genes and gene-regulatory sequences in a genome. List and describe characteristics of a genome that are hallmarks for identifying genes in an unknown sequence. What characteristics would you look for in a bacterial genome? A eukaryotic genome?

Consider the phylogenetic trees below pertaining to three related species (A, B, C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene Z, gene duplications have occurred in all species. Define orthology and paralogy relationships for the different Z genes. <>

Consider the phylogenetic trees below pertaining to three related species (A, B, C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene Y, a gene duplication occurred in the lineage leading to A after it diverged from that, leading to B and C. Are genes AY1 and AY2 orthologous or paralogous? Are genes AY1 and BY orthologous or paralogous? Are genes BY and CY orthologous or paralogous? <>

Consider the phylogenetic trees below pertaining to three related species (A, B, C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene X, no gene duplications have occurred in any lineage, and each gene X is derived from the ancestral gene X via speciation events. Are genes AX, BX, and CX orthologous, paralogous, or homologous? <>

You have isolated a gene that is important for the production of milk and wish to study its regulation. You examine the genomes of human, mouse, dog, chicken, pufferfish, and yeast and note that all genomes except yeast have an orthologous gene.

What does the existence of orthologous genes in chicken and pufferfish tell you about the function of this gene?

You have isolated a gene that is important for the production of milk and wish to study its regulation. You examine the genomes of human, mouse, dog, chicken, pufferfish, and yeast and note that all genomes except yeast have an orthologous gene.

How would you identify the regulatory elements important for the expression of your isolated gene in mammary glands?

When the human genome is examined, the chromosomes appear to have undergone only minimal rearrangement in the 100 million years since the last common ancestor of eutherian mammals. However, when individual humans are examined or when the human genome is compared with that of chimpanzees, a large number of small indels and SNPs can be detected. How are these observations reconciled?

Symbiodinium minutum is a dinoflagellate with a genome size that encodes more than 40,000 protein-coding genes. In contrast, the genome of Plasmodium falciparum has only a little more than 5000 protein-coding genes. Both Symbiodinium and Plasmodium are members of the Alveolate lineage of eukaryotes. What might be the cause of such a wide variation in their genome sizes?