Imagine that you are the head of a genome project to analyze the genome of a pre
ID: 141191 • Letter: I
Question
Imagine that you are the head of a genome project to analyze the genome of a previously uncharacterized species of a tardigrade. Since this is an imaginary project, you can also imagine that you have as much money as you need, with all of the necessary equipment and qualified and contented colleagues to carry out the analysis. You and members of your lab have recently completed the sequencing of more than 250,000 ESTs or partial transcripts from this species, using many different developmental stages and ages as your source material. You have also been actively sequencing the genome itself so that these ESTs can be located and analyzed, although some of the genome sequence is not yet done.
a. What is a tardigrade and what biological or evolutionary questions might be approached from an analysis of its genome? What arguments would you use to persuade your investors and the grant-awarding agencies that the tardigrade genome project is worth pursuing?
b. What is some of the information you will obtain from genome sequencing that you will not obtain from sequencing ESTs?
c. What is some of the information will you obtain by sequencing ESTs that you will not get from sequencing the genome itself?
d. Describe how you will use the ESTs in combination with the genome sequence to identify protein-coding genes and begin to annotate the genome.
*Genetics- please answer in great detail
Explanation / Answer
a. Tardigrades are one of the most indestrucitble microscopic species which can withstand even damaging radiations. A very ancient species which diverged from animals in pre-cambrian period evolved into its own unique species. Also called as water bears or water mosses, these are eight-legged and scaled micro-organisms that can even survive in space, extreme weather conditions like freezing conditions for more than a decade, dehydration,radiations and thus also called as extremophiles. Given its unique characterstics, it might be a interesting study to learn the genetic evolution of these organisms. Like how the unique genes are acquired by horizontal gene transfers from other species or its own evolution. If the genome is result of other such ancestral or closely related species. Biologically, how these genes or genetic make-up responds to environment, which transcripts or proteins are expressed at which stimuli, what pathways and mechanisms are involved.
Arguments for investors for funding might be supported by recent dsup protein finding by a research group which allows tardigradeto survive extreme radiations. When human cells were incorporated with this protein, it made those cells radiation ressistant. Thus, studying the genomics of tardigrade can help in finding potential applications to cellular preservation methods, genomic therapies, and the burgeoning science of transgenics.
b. Genome sequencing provides a complete picture of the genome, whereas ESTs only provide information of the transcripts expressed under a time-point. Genome sequencing would allow to study gene-structures, re-arrangements, transposons, and other genetic make-up whereas ESTs just allow to study exons in the genome.
c. ESTs or expressed sequence tags at differernt time points reveal the information about which gene or transcripts are expressed in which environmental, physilogical and biological condition. Thus, genetic responsiveness can be measured by sequencing ESTs. Aslo, complete gene structures, alternative transcripts,total transcriptome and proteome can be figured out by studying ESTs which is hard to determine by sequencing only.
d. ESTs in combination with genome sequences can help in identifying the complete genomic regions that comprises the genes. Having ESTs makes it easier to cover repetitive regions, complete the transcripts across the genomes and assembling the genome. This cumulative approach will help in finalising the complete genestructure and thus, genome annotation can be done.