This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Comparative Genomics”.
1. Which of the following is untrue about comparative genomics?
a) It is comparison of whole genomes from different organisms
b) It includes comparison of gene number, gene location, and gene content from these genomes
c) It provides insights into the mechanism of genome evolution and gene transfer among genomes
d) It doesn’t help to reveal the extent of conservation among genomes
View Answer
Explanation: It helps to understand the pattern of acquisition of foreign genes through lateral gene transfer. It also helps to reveal the core set of genes common among different genomes, which should correspond to the genes that are crucial for survival. This knowledge can be potentially useful in future metabolic pathway engineering.
2. Which of the following is untrue about Whole Genome Alignment?
a) This helps to reveal the presence of conserved functional elements
b) It doesn’t help to understand sequence conservation between genomes
c) It be accomplished through direct genome comparison or genome alignment
d) The alignment at the genome level is fundamentally no different from the basic sequence alignment
View Answer
Explanation: Regular alignment programs tend to be error prone and inefficient when dealing with long stretches of DNA containing hundreds or thousands of genes. Another challenge of genome alignment is effective visualization of alignment results. Because it is obviously difficult to sift through and make sense of the extremely large alignments, a graphical representation is a must for interpretation of the result.
3. Which of the following is untrue about LAGAN?
a) It stands for Limited Area Global Alignment of Nucleotides
b) It is a web-based program designed for pairwise alignment of small fragments of genomes only
c) It first finds anchors between two genomic sequences using an algorithm that identifies short, exactly matching words
d) Regions that have high density of words are selected as anchors
View Answer
Explanation: It is a web-based program designed for pairwise alignment of large genomes. The unique feature of this program is that it is able to take into account degeneracy of the genetic codes and is therefore able to handle more distantly related genomes.
4. A minimal constitutes genome, which is a _____ set of genes required for maintaining a free living cellular organism.
a) maximum
b) maximal
c) highest number of set of
d) minimal
View Answer
Explanation: Finding minimal genomes helps provide an understanding of genes constituting key metabolic pathways, which are critical for a cell’s survival. This analysis involves identification of orthologous genes shared between a number of divergent genomes.
5. Coregenes is a web-based program that determines a ________ set of genes based on comparison of ________ small genomes.
a) vast, four
b) core, fifteen
c) core, four
d) vast, fifteen
View Answer
Explanation: The user supplies NCBI accession numbers for the genomes of interest. The program performs an iterative BLAST comparison to find orthologous genes by using one genome as a reference and another as a query. This pairwise comparison is performed for all four genomes. As a result, the common genes are compiled as a core set of genes from the genomes.
6. Which of the following is untrue about Lateral gene transfer?
a) It is also known as vertical gene transfer
b) There is exchange of genetic materials between species
c) It mainly occurs among prokaryotic organisms when foreign genes are acquired through mechanisms
d) It is one of the examples is transformation
View Answer
Explanation: It is defined as the exchange of genetic materials between species in a way that is incongruent with commonly accepted vertical evolutionary pathway. Examples are transformation (direct uptake of foreign DNA from environment), conjugation (gene uptake through mating behavior), and transduction (gene uptake mediated by infecting viruses). The transmission of genes between organisms can occur relatively recently or as a more ancient event.
7. A way to discern lateral gene transfer is through phylogenetic analysis, referred to as an ‘among-genome’ approach, which can be used to discover __________
a) recent lateral gene transfer events but almost negligible ancient events
b) recent lateral gene transfer events
c) ancient lateral gene transfer events
d) both recent and ancient lateral gene transfer events
View Answer
Explanation: Abnormal groupings in phylogenetic trees are often interpreted as the possibility of lateral gene transfer events. There are some basic tools for identifying genomic regions that may be a result of lateral gene transfer events using the within-genome approach, namely, ACT, Swaap.
8. Within-Genome Approach is to identify regions within a genome with unusual compositions.
a) True
b) False
View Answer
Explanation: Single or oligonucleotide statistics, such as G–C composition, codon bias, and oligonucleotide frequencies are used. Unusual nucleotide statistics in certain genomic regions versus the rest of the genome may help to identify “foreign” genes in a genome. A commonly used parameter is GC skew ((G − C)/(G + C)), which is compositional bias for G in a DNA sequence and is a commonly used indicator for newly acquired genetic elements.
9. Which of the following is untrue about Gene Order Comparison?
a) When the order of a number of linked genes is conserved between genomes, it is called synteny
b) Generally, gene order is much more conserved compared with gene sequences
c) Generally, gene order is much less conserved compared with gene sequences
d) It is in fact rarely observed among divergent species
View Answer
Explanation: Gene order conservation is in fact rarely observed among divergent species. Therefore, comparison of syntenic relationships is normally carried out between relatively close lineages. However, if syntenic relationships for certain genes are indeed observed among divergent prokaryotes, they often provide important clues to functional relationships of the genes of interest.
10. Genes involved in the same metabolic pathway tend to be clustered among phylogenetically diverse organisms.
a) True
b) False
View Answer
Explanation: The preservation of the gene order is a result of the selective pressure to allow the genes to be co-regulated and function as an operon. Furthermore, the synteny of genes from divergent groups often associates with physical interactions of the encoded gene products.
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