Genome Size and the Evolution of New Genes

Despite the simple nature of the genetic code, there is considerable variation in terms of genome size, from the smallest known genomes - including the proteobacterium Candidatus Carsonella ruddii at less than 160 thousand base pairs, to the largest, such as the Japanese flowering plant Paris japonica at around 150 billion.
 
Despite these extremes, bacteria and archaea generally have around 3,000 genes within their genomes. Because prokaryotes have almost no non-coding sequences, this means that their genomes can be relatively small compared to those of eukaryotes. Smaller genomes also mean less to replicate at each round of cell division - which makes logistical sense for fast reproduction.

Eukaryotes typically have somewhere in the region of 20,000 genes, but their genomes are punctuated by long stretches of non-coding sequence - meaning their genome size does not necessarily translate to complexity. 

Paris japonica’s genome may be over fifty times the size of the human genome - but this is due at least in part to vast amounts of non-coding sequence and probably high levels of duplication - not necessarily more novel genes.

So how do organisms evolve new genes? The answer is typically by modifying the sequence that already exists.

One of the primary resources for new genes to evolve is through gene duplication. Imagine a section of DNA containing a gene is accidentally duplicated. Now the organism has a second copy of an existing gene. 

Such new gene copies are free from the constraints placed on the original to maintain function, and so they can diverge - potentially evolving a novel role or a modified function of the original. 

Another way to create new genes is DNA shuffling - where segments of an existing gene or gene copy are separated and moved to join those of a different gene - making a hybrid gene that can take on a new function.

Intragenic mutation - the changes in a gene sequence introduced by mutations over time, accounts for many “new” genes. This divergence which is most noticeable when comparing species or lineages which are themselves diverging independently. Once this divergence is beyond a certain point, or one gene takes on a novel function, they may be classified as different genes entirely.

Finally, horizontal gene transfer brings in novel genes and sequences to the genome from external sources - such as other individuals and even other species. This type of novel gene acquisition is most common in prokaryotes and archaea, with the transfer of antibiotic resistance genes being a well-known example. 

While rare in eukaryotes, it is still considered to be an essential source of genetic novelty, and genetic material can even come from distantly related species, such as the bacteria and fungi in this example.