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Question

You are studying a new primate species which you have just discovered in remote jungles of Africa.
You have brought back to the lab a lot cells that can be grown and used to isolate cellular components.
The standard methodology is to isolate random fragments of DNA, clone them, and do lots and lots of
sequencing to characterize the genome. You have already cloned restriction fragments in the size range
300-2000 bps but haven't yet sequenced them. Unfortunately, the Flat Earth Luddites (an
ultraultraconservative group) has decided biological knowledge is dangerous and managed to destroy
all the manufacturing plants for ddNTPs halting all large-scale sequencing projects.

Science must go on. Describe 5 experiments you will do do characterize the genome of this
primate. You can choose any genome-specific reasonable metrics. Include at least one that allows you
to make comparisons of it to the human, chimpanzee, and/or rhesus macaque (the genomes of these
primates are fully sequenced). Assume you can get any research materials from those organisms. You
can perform about a total of 10 kb of sequencing with dNTPs you have left over.

Answer 1

Sequence all subcloned fragments.
Analyze the cloned sequence for possible open reading frame sequence or regulatory sequences using SeqWeb GCG, pattern finder, etc. Look for clade specific repeat patterns. Characterize for mutations in all available sequence to clarify phylogenetic relationships, does not require coding sequence.

Southern- Label short isolated fragments of the new species using a distinct sequence if found. Make a genomic zoo blot with DNA from all species available both those with possible phylogenic proximity and those without as control. Probe the blot with species sequence of interest. Conserved DNA will allow probe binding only in related species with stringent washes.

Isolate RNA from the collected & cultured cells. Do northern blot. Probe cross species with possible orthologous primate sequence.

Create a genomic library from new species in phage. Plate and probe with conserved cDNA sequence from orthologous species. Pull out clones, if found. Make DNA of each & map for overlapping restrictions. Blot restriction digests & probe for 5' end, 3' prime end, and for intermediate exons to map clones exon boundaries.

Isolate exonic fragments and do a karyotype spread for chromosomal location with FISH or SKY.