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Monday, March 06, 2017

What's in Your Genome? Chapter 2: The Big Picture

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 2.

Chapter 2: The Big Picture
  • How much of the genome has been sequenced?
  • Whose genome was sequenced?
  • How many genes?
  • Pseudogenes
  • Regulatory sequences
  • Origins of replication
  • Centromeres
  • Telomeres
  • Scaffold Attachment regions (SARs)
  • Transposons
  • Viruses
  • Mitochondrial DNA (NumtS)
  • How much of our genome is functional?


John Harshman said...

Why capitalize the "s" in "Numts"? Hey, does the human genome have any tandem repeats of whole mt genomes? I seem to recall that some bird species do.

TheOtherJim said...

Last time I checked, the largest human Numts were still less than the whole genome. Nothing as wild as the birds...

(my comment based on this paper).

TheOtherJim said...

Are you thinking of the cat?

JV Lopez, N Yuhki, R Masuda, W Modi, SJ OBrien
Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat
J Mol Evol, 39 (1994), pp. 174–190 95018295

judmarc said...

Why capitalize the "s" in "Numts"?


Mikkel Rumraket Rasmussen said...

Can I order a signed copy? :)

Larry Moran said...

Why capitalize the "s" in "Numts"?

There are many different ways of writing the term. Do you have a particular reason for preferring NUMTs, Numts, NUMTS, or numts?

Lang, M., Sazzini, M., Calabrese, F. M., Simone, D., Boattini, A., Romeo, G., ... & Gasparre, G. (2012). Polymorphic NumtS trace human population relationships. Human genetics, 131(5), 757-771.

Bintz, B. J., Dixon, G. B., & Wilson, M. R. (2014). Simultaneous Detection of Human Mitochondrial DNA and Nuclear‐Inserted Mitochondrial‐origin Sequences (NumtS) using Forensic mtDNA Amplification Strategies and Pyrosequencing Technology. Journal of forensic sciences, 59(4), 1064-1073.

Calabrese, F. M., Balacco, D. L., Simone, D., & Attimonelli, M. (2012). NumtS footsteps from the past: an interbreed between eukaryotic nucleus and the mitochondrion. EMBnet. journal, 18(A), p-82.

Calabrese, F. M., Simone, D., & Attimonelli, M. (2012). Primates and mouse NumtS in the UCSC Genome Browser. BMC bioinformatics, 13(4), S15.

John Harshman said...

I don't understand the rationale for that particular orthography. I would understand "NuMtS", though I prefer just "numts". And of course the singular is "numt".

Federico Abascal said...

Looks very interesting!
I'd add a section "How many proteins?"
And if I were to write it I would dedicate a section to the "adaptive immunity" against transposons (piRNAs) :-)
The things that happen to cancer genomes are also of interest to me.