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Understanding the Role of Transposons in Evolution: Are They Selfish or Essential?

This study investigates the ubiquity and abundance of transposons in genomes, addressing the question of whether they are selfish entities or essential for life. We analyze the representation of transposons across various genomic sets and their relationship with environmental gene tags in metagenomes. By examining the prevalence and function of transposons, we explore the idea that 'cheaters' may have evolutionary advantages. The findings highlight the paradoxical nature of certain proteins, like the hypothetical protein and RuBisCo, in their abundance and essentiality in different life forms.

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Understanding the Role of Transposons in Evolution: Are They Selfish or Essential?

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  1. Are transposons selfish? Ramy Aziz Rob Edwards

  2. What does it mean to “win”? • Ubiquity: (omnipresence/ universality essentiality) • For the purpose of this study, the ubiquity of x is calculated as the number of “sets” to which x belongs • x= (gene, protein, function, protein-encoding gene, enzyme) • @sets = (genomes, metagenomes, biomes) • Abundance: (profusion  ‘fertility/ promiscuity’) • The abundance of x is calculated as the (average) number of times x is represented in a particular set

  3. Counting CDS in genomes ☺ CDS fully sequenced ☺ one copy per function (more == paralogs) So, just collect all genomes, extract all cds, count functions, and get results. ☹ Sequenced genomes do not represent life, but rather human-centered interests in life.

  4. Counting EGTs in metagenomes • Environmental gene tag (EGT) comes from one organism and represents one or more functions. • ☺ Counts ∝ abundance • ☹ Counts depend on: • Abundance • Gene length • Metagenome sample size ($$) ☹ Up 90% with no BLAST hits

  5. Biology Textbooks • The most abundant protein: RuBisCo* • How so? It’s the enzyme with the highest copy number in ecosystems (or with highest total mass). • Is it the most ubiquitous? No! It’s almost only in photosynthetic organisms. • Is its gene the most abundant? No! Most genomes lack it. *ribulose-1,5-bis phosphate carboxylase

  6. And the winner is … • Hypothetical protein • aka • Conserved protein • Unknown protein • Protein predicted by Glimmer • Very hypothetical protein • No name

  7. Why transposons? • Essential for life • Cheaters win Two hypotheses:

  8. Metagenomes … fertility Pearson Corr. 0.524 eco-essentiality

  9. Metagenomes … fertility Habitat -specific Life essentials Pearson Corr. 0.524 eco-essentiality

  10. Transposons prefer prophages

  11. Tn per prophage 30 All phages Number of phage Defective phages 20 Suspected viable phages 10 Viable phages 0 2 4 6 8 10 12 14 16 Number of Tn per phage

  12. Why transposons? • Essential for life ✔ • Cheaters win ? Two hypotheses:

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