Decoding the building blocks of life

What’s in a genome?

This is a post I’ve been intending to write for a little while now and was inspired by a brilliant, comprehensive guide to genome science by the science communication team at the Earlham Institute in Norwich [1]. A genome of an organism is all the genetic material that is required to encode the functioning of that individual. To understand their construction, scientist conduct sequencing, a process of deciphering the order of DNA, the building blocks of a genome. In the article, the author provides a nice analogy for understanding how DNA relates to the genome and the living organism. They equate producing a genome to how a composer produces a symphony: notes (DNA) – instruments (RNA) – Melody (Protein) – Musical Score (Genome) – Symphony (Living organism).

 

The first genome of any organism, the bacterium Haemophilus influenzae, was completed in 1995 [2]. In the next ten year, many notable species were sequenced including the fruit fly (Drosophila melanogaster (2000)), thale cress (Arabidopsis thaliana (2000)) and the mosquito (Anopholes gambaie (2002)). The human genome was published in 2003 but took 13 years to sequence costing approximately $3 billion [3].

Since then, there has been a rapid increase in sophisticated technology and scientific effort to produce genomes representing a broad range of taxa, for example, a human genome can now be sequenced for around $1000. Genomes are an integral component of my PhD project and this revolution of sequencing and construction has made my current research feasible.

All shapes and sizes – what can be learned from studying plant genomes? 

The more we understand genomes, the more their variety astounds us. In my field of research, plant genomics, recent progress has revealed the diversity of plant genomes. Paris Japonica, a native Japanese species, was recently revealed to have the largest genome of any organism (150 billion base pairs), greater than the previous record holder, the marbled lungfish, Protopterus aethiopicus (130 billion base pairs) [4]. If the DNA of one cell of Paris japonica was stretched out, it would reach 91m in length. On the flip side, Genlisea tuberosa, a carnivorous plant, has the smallest plant genome (61 million base pairs).

 

This represents a roughly 2500 fold increase in size between the smallest and largest plant genome. How can Genlisea tuberosa still function as a plant with such little DNA? Or perhaps the question should be that why and what advantage does having so much DNA offer Paris japonica? Is it costly to maintain such a large genome? These are just some of the questions that still being asked by the scientists with no clear answers.

Utricularia gibba, an aquatic carnivorous plant closely related to Genlisea tuberosa, has a comparably small genome (82 million base pairs). Its genome contains the majority of the normal genes contained within a plant [5]. 97% of the genome codes for proteins with only 3% considered as ‘junk DNA’. When compared to the human genome which is estimated at 97% ‘junk DNA’ and 3% coding genes, this variation becomes obvious. The lack of DNA does not make these organisms any less complex or interesting. Taking the musical analogy a little further, this is equivalent to asking how can a composer use so few notes (DNA) but still make a complete symphony.

 

By studying over 300 plant genomes already produced and making comparisons between them, scientists hope to address important biological questions: Do all plants have the same genes (Do all symphonies have common strings of notes)? and Why are some genomes bigger than others (Why are some symphonies longer than others)? Genome and genetic science is the next frontier of deciphering the biology of all living organisms and will allow us to understand the world around us in greater depth than ever before. What is becoming apparent is that the further we delve into the complexities of genomes, the greater number of questions can be answered (as well as new ones being asked).

If you want to learn more:

  1. Bickerton, P. (2017). What’s in a genome? http://www.earlham.ac.uk/articles/whats-genome.
  2. Fleischmann, R. D. et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269(5223). 496-512.
  3. Noble, I. (2003). Human genome finally complete. http://news.bbc.co.uk/1/hi/sci/tech/2940601.stm.
  4. Pellicer, J. et al. (2010). The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society, 164(1). 10–15.
  5. Ibarra-Laclette, E. et al. (2013). Architecture and evolution of a minute plant genome. Nature, 498. 94–98.

 

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