Topic 4 - Dynamic Genomes Flashcards
Define synteny
The term used to describe the preserved order of genes along a chromosome, or region of chromosome, indicative of a shared common ancestral chromosome.
Define paleoploidy
The state of genome or chromosome ploidy in evolutionary common ancestral organisms implied by the genome analysis of present-day organisms.
Define paralogues
Genes within the same species that share a common ancestor through duplication event.
What features of DNA sequence contribute to the differences in C-value between organisms?
You may have thought of highly repetitive sequences (often called satellites and microsatellites), the presence of introns, RNA-encoding genes and transposons.
What are Pseudogenes?
Non-functional copies of a gene, which, if transcribed, produce an inactive protein.
What is pseudotetraploid?
The state of an organism’s genome reflecting incomplete tetraploidy, often through chromosome loss. Organisms can become tetraploid (i.e. have two sets of their diploid genome) by alloploidy (the two sets originate in ancestrally related, but separate species) or autoploidy (the two sets originating in the same species).
What is the function of histone proteins?
Histones are protein components of chromosomes; they assemble to form a multimeric complex around which the DNA winds as part of the compaction process to form a chromosome.
Within which cellular areas are ribosomes found in a eukaryote?
Ribosomes are found at the rough endoplasmic reticulum and also in the cytosol.
Recall an example of a polyploid organism
An example might be the hexaploid common wheat, and also the pseudotetraploid X. laevis.
In addition to the order of genes along a chromosome, which other feature of genes could be used for comparisons when looking for synteny? (Hint: Consider how the coding region of a gene is split.)
The position of introns and exons, as well as transcriptional orientation, in regions of synteny, would also be expected to be similar.
In addition to the order of genes along a chromosome, which other feature of genes could be used for comparisons when looking for synteny? (Hint: Consider how the coding region of a gene is split.)
The position of introns and exons, as well as transcriptional orientation, in regions of synteny, would also be expected to be similar.
Which two lines of evidence based upon gene/protein sequence and chromosome structure can provide evidence for duplication events?
Comparison programmes such as BLAST, which identify genes/proteins of similar sequence and synteny, can be used to identify conserved gene order, both indicative of duplication events.
What is the 2R hypothesis?
The hypothesis, now accepted, that the evolution of vertebrates involved two whole genome duplications (WGDs).
Recall the meaning of the term synteny.
Synteny is the shared order of genes along a stretch of an ancestral chromosome that is shared in the descendants from that common ancestor.
What are orthologues?
This term is used to describe all genes that are derived from a common ancestral gene that are found in different species. These often retain the same function in both species. For example, the human β-globin gene and the mouse β-globin genes are orthologues. Similarly, the mouse FEN1 gene and human FEN1 gene are orthologues.
What are paralogues?
Genes that are within the same species that have arisen from a common ancestor through a duplication event. As an example, the mouse β-globin and α-globin genes are paralogues.
What are homologues?
Homologues: Genes that are related to each other by descent from a common ancestral gene; these can be either paralogues or orthologues. It is usual to describe such genes in terms of being homologues, and then to express the similarity in terms of percentage identity.
What are ohnologues?
Ohnologues: Genes that are related to each other through WGD events. This term derives from the name of the scientist (Susumu Ohno) who originally suggested WGD as a major mechanism through which present-day genomes had evolved (Ohno, 1970).
What name is given to DNA sequences that closely resemble genes, but which are non-functional, often with frameshift and stop mutations?
Pseudogenes
Within gene duplication what does neo-functionalisation mean?
Following a gene duplication, one of the resulting genes acquires a distinct role due to the acquisition of sequence changes.
Within gene duplication what does sub-functionalisation mean?
Following a gene duplication, the two resulting genes acquire distinct roles by sequence divergence, leading to each gene losing a complementary subset of the original roles of the ancestral gene.
What does duplication-degeneration-complementation (DDC) mean?
Another term used in place of sub-functionalisation, as applied to the fate of duplicated gene. Duplication of a gene is followed by differences arising in each derivative (degeneration) and functions that are complementary each other.
Recall what is meant by paralogues.
Paralogues are genes within the same species (in this case zebrafish) that share a common ancestor through a duplication event.
What process is unequal cross-over associated with?
Gene duplication, such as events that occur at clusters of genes of similar nucleotide sequence.
